PlantCellCultureProtocolsLoyola Vargas&Ochoa AlejoHumanaPress2012 (1)

METHODS

IN

MOLECULAR BIOLOGY™

Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK

For further volumes: http://www.springer.com/series/7651

Plant Cell Culture Protocols Third Edition Edited by

Víctor M. Loyola-Vargas Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México

Neftalí Ochoa-Alejo Departamento de Ingeniería Genética de Plantas, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del I.P.N., Irapuato, Guanajuato, México; Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del I.P.N., Irapuato, Guanajuato, México

Editors Víctor M. Loyola-Vargas Unidad de Bioquímica y Biología Molecular de Plantas Centro de Investigación Científica de Yucatán Mérida, Yucatán, México

Neftalí Ochoa-Alejo Departamento de Ingeniería Genética de Plantas Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del I.P.N. Irapuato, Guanajuato, México and Departamento de Biotecnología y Bioquímica Unidad Irapuato Centro de Investigación y de Estudios Avanzados del I.P.N. Irapuato, Guanajuato, México

ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-817-7 e-ISBN 978-1-61779-818-4 DOI 10.1007/978-1-61779-818-4 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2012936126 © Springer Science+Business Media, LLC 2012 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Human Press is part of Springer Science+Business Media (www.springer.com)

Preface Cell culture methodologies have become standard procedures in most plant laboratories. Today, facilities for in vitro cell cultures are found in practically each plant biology laboratory, serving different purposes since tissue culture has turned into a basic asset for modern biotechnology, from the fundamental biochemical aspects to the massive propagation of selected individuals. The subject of this book is taught around the world as part of undergraduate and graduate courses in agronomical and biological sciences. However, the apparent simplicity of cell culture technology should not lead to mistakingly consider it as trivial. It would be very difficult to understand modern plant biotechnology without in vitro cell cultures and even today, the application of recombinant DNA technology to important crops is hampered by the poor embryogenic or morphogenetic response of in vitro cultured tissues. This third edition of Plant Cell Culture Protocols follows a similar plot as its predecessors. It also pursues similar goals, i.e., to provide an updated step-to-step guide to the most common and applicable techniques and methods for plant tissue and cell culture. A total of 29 chapters, divided into five major sections, have been included. Topics selected cover from general methodologies, such as culture induction, growth and viability evaluation, statistical analysis and contamination control, to highly specialized techniques, such as clonal propagation, haploid production, somatic embryogenesis, organelle transformation, passing through the laborious process to measure the epigenetic changes in tissue cultures. The protocols are currently used in the research programs of the authors or represent important parts of business projects aimed to generate improved plant materials. Two appendices have also been included; the first of them discusses common principles for the formulation of culture media and also lists the composition of the eight most commonly used media formulations. The second appendix compiles a list of useful Internet sites for cell culture scientists. A total of more than 100 sites have been selected, based on the quality of the information offered in them, as well as on their users’ friendliness. We hope that readers will find this version of Plant Cell Culture Protocols, which belongs to the Methods in Molecular Biology series, as a helpful source of information in their research projects, since this has been its real purpose. We would like to thank the authors of each chapter for responding to our constant requests for the materials, despite their reckless work schedules. They made us possible to carry this job to its completion. Finally, we should express our profound gratitude to Professor John Walker for his trust in our experience to complete this project. We have certainly enjoyed the opportunity to interact with colleagues from all over the world. Mérida, Yucatán, México Irapuato, Guanajuato, México

Víctor M. Loyola-Vargas Neftalí Ochoa-Alejo

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Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2 3

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An Introduction to Plant Cell Culture: The Future Ahead . . . . . . . . . . . . . . . . . . . Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo History of Plant Tissue Culture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Trevor Thorpe Callus, Suspension Culture, and Hairy Roots. Induction, Maintenance and Characterization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Rosa M. Galáz-Ávalos, Sagrario Aguilar-Díaz, Pedro A. Xool-González, Silvia M. Huchín-May, and Víctor M. Loyola-Vargas Growth Measurements: Estimation of Cell Division and Cell Expansion . . . . . . . . . Gregorio Godoy-Hernández and Felipe A. Vázquez-Flota Measurement of Cell Viability. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lizbeth A. Castro-Concha, Rosa María Escobedo, and María de Lourdes Miranda-Ham Pathogen and Biological Contamination Management in Plant Tissue Culture: Phytopathogens, Vitro Pathogens, and Vitro Pests . . . . . . . . . . . . . Alan C. Cassells Cryopreservation of Embryogenic Cell Suspensions by Encapsulation–Vitrification and Encapsulation–Dehydration . . . . . . . . . . . . . . . Zhenfang Yin, Long Chen, Bing Zhao, Yongxing Zhu, and Qiaochun Wang The Study of In Vitro Development in Plants: General Approaches and Photography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Edward C. Yeung Use of Statistics in Plant Biotechnology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Michael E. Compton Tissue Culture Methods for the Clonal Propagation and Genetic Improvement of Spanish Red Cedar (Cedrela odorata) . . . . . . . . . . . . . . . . . . . . . . Yuri Peña-Ramírez, Juan Juárez-Gómez, José Antonio González-Rodríguez, and Manuel L. Robert Micropropagation of Banana . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Yıldız Aka Kaçar and Ben Faber Liquid In Vitro Culture for the Propagation of Arundo donax . . . . . . . . . . . . . . . . Miguel Ángel Herrera-Alamillo and Manuel L. Robert Production of Haploids and Doubled Haploids in Maize . . . . . . . . . . . . . . . . . . . . Vanessa Prigge and Albrecht E. Melchinger

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Maize Somatic Embryogenesis: Recent Features to Improve Plant Regeneration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Verónica Garrocho-Villegas, María Teresa de Jesús-Olivera, and Estela Sánchez Quintanar Improved Shoot Regeneration from Root Explants Using an Abscisic Acid-Containing Medium . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Subramanian Paulraj and Edward C. Yeung Cryopreservation of Shoot Tips and Meristems: An Overview of Contemporary Methodologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Erica E. Benson and Keith Harding Anther Culture of Chili Pepper (Capsicum spp.) . . . . . . . . . . . . . . . . . . . . . . . . . . . Neftalí Ochoa-Alejo Production of Interspecific Hybrids in Ornamental Plants. . . . . . . . . . . . . . . . . . . . Juntaro Kato and Masahiro Mii Plant Tissue Culture of Fast-Growing Trees for Phytoremediation Research . . . . . . José Luis Couselo, Elena Corredoira, Ana M. Vieitez, and Antonio Ballester Removing Heavy Metals by In Vitro Cultures . . . . . . . . . . . . . . . . . . . . . . . . . . . . María del Socorro Santos-Díaz and María del Carmen Barrón-Cruz Establishment of a Sanguinarine-Producing Cell Suspension Culture of Argemone mexicana L (Papaveraceae): Induction of Alkaloid Accumulation . . . . Felipe A. Vázquez-Flota, Miriam Monforte-González, Cecilia Guízar-González, Jorge Rubio-Piña, and Karen Trujillo-Villanueva Epigenetics, the Role of DNA Methylation in Tree Development . . . . . . . . . . . . . . Marcos Viejo, María E. Santamaría, José L. Rodríguez, Luis Valledor, Mónica Meijón, Marta Pérez, Jesús Pascual, Rodrigo Hasbún, Mario Fernández Fraga, María Berdasco, Peter E. Toorop, María J. Cañal, and Roberto Rodríguez Fernández The Potential Roles of microRNAs in Molecular Breeding . . . . . . . . . . . . . . . . . . . Qing Liu and Yue-Qin Chen Determination of Histone Methylation in Mono- and Dicotyledonous Plants . . . . . Geovanny I. Nic-Can and Clelia De la Peña Basic Procedures for Epigenetic Analysis in Plant Cell and Tissue Culture . . . . . . . . José L. Rodríguez, Jesús Pascual, Marcos Viejo, Luis Valledor, Mónica Meijón, Rodrigo Hasbún, Norma Yague Yrei, María E. Santamaría, Marta Pérez, Mario Fernández Fraga, María Berdasco, Roberto Rodríguez Fernández, and María J. Cañal Plant Tissue Culture and Molecular Markers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . María Tamayo-Ordoñez, Javier Huijara-Vasconselos, Adriana Quiroz-Moreno, Matilde Ortíz-García, and Lorenzo Felipe Sánchez-Teyer Biolistic- and Agrobacterium-Mediated Transformation Protocols for Wheat . . . . . Cecília Tamás-Nyitrai, Huw D. Jones, and László Tamás

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Improved Genetic Transformation of Cork Oak (Quercus suber L.) . . . . . . . . . . . . . 385 Rubén Álvarez-Fernández and Ricardo-Javier Ordás 29 Organelle Transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401 Anjanabha Bhattacharya, Anish Kumar, Nirali Desai, and Seema Parikh 30 Appendix A: The Components of the Culture Media . . . . . . . . . . . . . . . . . . . . . . . 407 Víctor M. Loyola-Vargas 31 Appendix B: Plant Biotechnology and Tissue Culture Resources in the Internet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419 Víctor M. Loyola-Vargas Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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Contributors SAGRARIO AGUILAR-DÍAZ • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México YILDIZ AKA KAÇAR • Department of Horticulture, Faculty of Agriculture, Cukurova University, Adana, Turkey RUBEN ALVAREZ-FERNANDEZ • Department of Plant Sciences, University of Cambridge, Cambridge, UK ANTONIO BALLESTER • Instituto de Investigaciones Agrobiológicas de Galicia, C.S.I.C., Avenida de Vigo, s/n, Campus Sur, Santiago de Compostela, Spain MARÍA DEL CARMEN BARRÓN-CRUZ • Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP, México ERICA E. BENSON • Conservation, Environmental Science and Biotechnology, Damar, Cupar Muir, Fife, Scotland, UK MARÍA BERDASCO • Cancer Epigenetics and Biology Program, IDIBELL, Barcelona, Spain ANJANABHA BHATTACHARYA • National Environmental Sound Production Agriculture Laboratory, University of Georgia, Tifton, GA, USA MARÍA J. CAÑAL • Área de Fisiología Vegetal, Depto. BOS, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain; Instituto de Biotecnología de Asturias (asociado al CSIC), Oviedo, Spain ALAN C. CASSELLS • Department of Zoology, Ecology and Plant Science, University of Cork, Cork, Ireland LIZBETH A. CASTRO-CONCHA • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México LONG CHEN • College of Horticulture, Northwest Agricultural & Forest University, Yangling, Shaanxi, People’s Republic of China YUE-QIN CHEN • Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, People’s Republic of China MICHAEL E. COMPTON • School of Agriculture, University of Wisconsin-Platteville, University Plaza, Platteville, WI, USA ELENA CORREDOIRA • Instituto de Investigaciones Agrobiológicas de Galicia, C.S.I.C., Avenida de Vigo, s/n, Campus Sur, Santiago de Compostela, Spain JOSÉ LUIS COUSELO • Estación Fitopatológica do Areeiro, Subida a la Robleda, s/n, Pontevedra, Spain NIRALI DESAI • BenchBio, Vapi, Gujarat MARÍA TERESA DE JESÚS-OLIVERA • Plant Cell Tissue Culture Laboratory, Chemistry Faculty, UNAM, Mexico, D.F., Mexico

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CLELIA DE LA PEÑA • Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México ROSA MARÍA ESCOBEDO • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México BEN FABER • Agriculture & Natural Resources, University of California, Ventura, CA, USA ROBERTO RODRÍGUEZ FERNÁNDEZ • Área de Fisiología Vegetal, Depto. BOS, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain; Instituto de Biotecnología de Asturias (asociado al CSIC), Oviedo, Spain MARIO FERNÁNDEZ FRAGA • Department of Endocrinology and Nutrition Service, Hospital Universitario Central de Asturias, Oviedo, Spain ROSA M. GALÁZ-ÁVALOS • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México VERÓNICA GARROCHO-VILLEGAS • Laboratorio 103, Conjunto “E”, Paseo de la Investigación Científica, Circuito Institutos, Ciudad Universitaria, México D.F., México GREGORIO GODOY-HERNÁNDEZ • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México JUAN JUÁREZ-GÓMEZ • Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México JOSÉ ANTONIO GONZÁLEZ-RODRÍGUEZ • Instituto Tecnológico Superior de Acayucan, Acayucan, Veracruz, México CECILIA GUÍZAR-GONZÁLEZ • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México KEITH HARDING • Conservation, Environmental Science and Biotechnology, Damar, Drum Road, Cupar Muir, Fife, Scotland, UK RODRIGO HASBÚN • Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile MIGUEL ÁNGEL HERRERA-ALAMILLO • Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México SILVIA M. HUCHÍN-MAY • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México JAVIER HUIJARA-VASCONSELOS • Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México HUW D. JONES • Research Group Leader, Cereal Transformation Group, Centre for Crop Genetic Improvement, Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, UK JUNTARO KATO • Department of Biology, Aichi University of Education, Kariya, Japan ANISH KUMAR • BenchBio, Vapi, Gujarat QING LIU • Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, People’s Republic of China VÍCTOR M. LOYOLA-VARGAS • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México MÓNICA MEIJÓN • Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria

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ALBRECHT E. MELCHINGER • Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, Stuttgart, Germany MASAHIRO MII • Graduate School of Horticulture, Chiba University, Matsudo, Japan MARÍA DE LOURDES MIRANDA-HAM • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México MIRIAM MONFORTE-GONZÁLEZ • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México GEOVANNY I. NIC-CAN • Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, México NEFTALÍ OCHOA-ALEJO • Departamento de Ingeniería Genética de Plantas, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del I.P.N., Irapuato, Guanajuato, México; Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del I.P.N., Irapuato, Guanajuato, México RICARDO-JAVIER ORDÁS • Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain MATILDE ORTÍZ-GARCÍA • Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México SEEMA PARIKH • BenchBio, Vapi, Gujarat JESÚS PASCUAL • Área de Fisiología Vegetal, Depto. BOS, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain; Instituto de Biotecnología de Asturias (asociado al CSIC), Oviedo, Spain SUBRAMANIAN PAULRAJ • Biol Sci Dept, AB, University of Calgary, Calgary, Canada MARTA PÉREZ • Área de Fisiología Vegetal, Depto. BOS, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain; Instituto de Biotecnología de Asturias (asociado al CSIC), Oviedo, Spain YURI PEÑA-RAMÍREZ • Instituto Tecnológico Superior de Acayucan, Acayucan, Veracruz, México VANESSA PRIGGE • Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, Stuttgart, Germany ESTELA SÁNCHEZ QUINTANAR • Laboratorio 103, Conjunto “E”, Paseo de la Investigación Científica, Circuito Institutos, Ciudad Universitaria, México D.F., México ADRIANA QUIROZ-MORENO • Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México MANUEL L. ROBERT • Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México JOSÉ L. RODRÍGUEZ • Área de Fisiología Vegetal, Depto. BOS, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain; Instituto de Biotecnología de Asturias (asociado al CSIC), Oviedo, Spain JORGE RUBIO-PIÑA • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México LORENZO FELIPE SÁNCHEZ-TEYER • Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México MARÍA E. SANTAMARÍA • Department of Biology, WSC 339/341, The University of Western Ontario, Ontario, Canada

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MARÍA DEL SOCORRO SANTOS-DÍAZ • Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP, México MARCOS VIEJO • Área de Fisiología Vegetal, Depto. BOS, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain; Instituto de Biotecnología de Asturias (asociado al CSIC), Oviedo, Spain LÁSZLÓ TAMÁS • Department of Plant Physiology, Eötvös Loránd University, Budapest, Hungary CECÍLIA TAMÁS-NYITRAI • Centre for Agricultural Research, Hungarina Academy of Sciences, Martonvásár, Hungary; Óbuda University, Budapest, Hungary MARÍA TAMAYO-ORDOÑEZ • Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México TREVOR THORPE • Biological Sciences Department, University of Calgary, Calgary, AB, Canada T2N 1N4 PETER E. TOOROP • Seed Conservation Department, Royal Botanic Gardens Kew, Wakehurst Place, West Sussex, UK KAREN TRUJILLO-VILLANUEVA • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México LUIS VALLEDOR • Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, Austria FELIPE A. VÁZQUEZ-FLOTA • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México ANA M. VIEITEZ • Instituto de Investigaciones Agrobiológicas de Galicia, C.S.I.C., Avenida de Vigo, s/n, Campus Sur, Santiago de Compostela, Spain QIAOCHUN WANG • College of Horticulture, Northwest Agricultural & Forest University, Yangling Shaanxi, People’s Republic of China PEDRO A. XOOL-GONZÁLEZ • Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México EDWARD C. YEUNG • Biol Sci Depart, University of Calgary, Calgary, Canada ZHENFANG YIN • College of Horticulture, Northwest Agricultural & Forest University, Yangling Shaanxi, People’s Republic of China NORMA YAGUE YREI • Área de Fisiología Vegetal, Depto. BOS, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain; Instituto de Biotecnología de Asturias (asociado al CSIC), Oviedo, Spain BING ZHAO • College of Horticulture, Northwest Agricultural & Forest University, Yangling Shaanxi, People’s Republic of China YONGXING ZHU • College of Horticulture, Northwest Agricultural & Forest University, Yangling Shaanxi, People’s Republic of China

Chapter 1 An Introduction to Plant Cell Culture: The Future Ahead Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo Abstract Plant cell, tissue, and organ culture (PTC) techniques were developed and established as an experimental necessity for solving important fundamental questions in plant biology, but they currently represent very useful biotechnological tools for a series of important applications such as commercial micropropagation of different plant species, generation of disease-free plant materials, production of haploid and doublehaploid plants, induction of epigenetic or genetic variation for the isolation of variant plants, obtention of novel hybrid plants through the rescue of hybrid embryos or somatic cell fusion from intra- or intergeneric sources, conservation of valuable plant germplasm, and is the keystone for genetic engineering of plants to produce disease and pest resistant varieties, to engineer metabolic pathways with the aim of producing specific secondary metabolites or as an alternative for biopharming. Some other miscellaneous applications involve the utilization of in vitro cultures to test toxic compounds and the possibilities of removing them (bioremediation), interaction of root cultures with nematodes or mycorrhiza, or the use of shoot cultures to maintain plant viruses. With the increased worldwide demand for biofuels, it seems that PTC will certainly be fundamental for engineering different plants species in order to increase the diversity of biofuel options, lower the price marketing, and enhance the production efficiency. Several aspects and applications of PTC such as those mentioned above are the focus of this edition. Key words: Aseptic culture, Genetic modified organisms, Large-scale propagation, Metabolic engineering, Plant cell culture, Techniques

1. Introduction Plant cell, tissue, and organ culture (PTC) techniques were developed and established as an experimental necessity for solving important fundamental questions in plant biology, but they currently represent very useful biotechnological tools for a series of important applications such as commercial micropropagation of different plant species, generation of disease-free plant materials, production of haploid and double-haploid plants, induction of epigenetic or genetic variation for the isolation of variant plants, obtention of novel hybrid plants through the rescue of hybrid

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_1, © Springer Science+Business Media, LLC 2012

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embryos or somatic cell fusion from intra- or intergeneric sources, conservation of valuable plant germplasm, and is the keystone for genetic engineering of plants to produce disease and pest resistant varieties, to engineer metabolic pathways with the aim of producing specific secondary metabolites or as an alternative for biopharming. Some other miscellaneous applications involve the utilization of in vitro cultures to test toxic compounds and the possibilities of removing them (bioremediation), interaction of root cultures with nematodes or mycorrhiza, or the use of shoot cultures to maintain plant viruses. With the increased worldwide demand for biofuels, it seems that PTC will certainly be fundamental for engineering different plants species in order to increase the diversity of biofuel options, lower the price marketing, and enhance the production efficiency. Several aspects and applications of PTC such as those mentioned above are the focus of this edition. PTC technology also explores conditions that promote cell division and genetic reprogramming in in vitro conditions and it is considered an important tool in both basic and applied studies, as well as in commercial application (1). The theoretical basis for plant tissue culture was proposed by Gottlieb Haberlandt in 1902. He predicted that eventually a complete and functional plant could be regenerated from a single cell. Although all multicellular organisms share almost the same life cycle fate, plant cells in contrast with animal cells have the quality to be totipotents. This means that a single cell can become a complete plant and backwards, and all this is governed by a precise and regulatory mechanism during cell division. This regulation is what makes one organism different from another and roots from leaves. The knowledge of the events that govern the transformation of that single cell into a complete and functional individual lies at the core of the understanding of life itself. Recently, some of the regulatory steps that govern the totipotentiality and cell differentiation have been uncovered. PTC propitiate the best condition to induce or repress some key genes for the morphogenesis process, allowing the formation of new structures in vitro that otherwise cannot be formed under natural conditions. PTC is a set of techniques for the aseptic culture of cells, tissues, organs, and their components under defined physical and chemical conditions in in vitro aseptic and controlled environment (Fig. 1). Throughout the years, the techniques developed from the early 1960s to the mid-1980s (see Chapter 2) are found today in practically each plant biology laboratory and have turned into a basic asset to modern biotechnology. These tools are used for different purposes, from massive propagation of selected individuals to fundamental biochemical aspects.

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Fig. 1. (a) Callus from Coryphantha spp. (b) Suspension culture from Canavalia ensiformis. (c) Scale-up C. roseus suspension cultures. (d) Regeneration of Jatropha curcas plants from callus. (e) Protoplasts from Coffea arabica. (f) Somatic embryogenesis in Coffea canephora. (g) Root culture from Daucus carota. (h) Micropropagation of Agave fourcroydes. Pictures a, b, c, d, f, and g are from the authors’ laboratories. Pictures e and h are a gift from the laboratories of Dr. Teresa Hernández-Sotomayor and Dr. Manuel Robert, respectively, from Centro de Investigación Científica de Yucatán.

2. General Aspects of Cell, Tissue, and Organ Culture

It is of primary importance for those who are using plant tissue culture techniques for the first time to know about the history of those researchers whose contributions led to the development of these experimental systems and biotechnological tools. Professor Thorpe (Chapter 2) had written a wonderful article about the main historical facts in PTC advances. The basic principles of in vitro plant tissue culture involve the selection of the adequate explant from a plant source, the subsequent surface sterilization to eliminate microbial contaminants,

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inoculation in a proper culture medium to allow growth and differentiation of the tissue, incubation under controlled conditions, and finally the adaptation of in vitro regenerated plants to greenhouse conditions. Different culture systems are usually used such as cell cultures (cell suspensions and protoplasts), tissue cultures (callus and differentiated tissues), and organ cultures (anthers, embryos, meristems, shoots, and roots). These systems are applied for several basic and biotechnological goals, as mentioned before. Some aspects of the general procedures, basic principles, and applications of PTC have been included in this edition (see Chapters 3–6).

3. Plant Micropropagation After the demonstration of totipotency in plants, the potential of PTC for vegetative or clonal propagation was first recognized. Clonal propagation implies that the same genetic background of donor plants is maintained through the next plant generations. Although micropropagation techniques are theoretically applied to all plant species, they are recommended for those species that are usually asexually propagated or in cases of seed-recalcitrant species. Undoubtedly, micropropagation has been the most important commercial application of in vitro cultures, and many companies worldwide are currently producing millions of clonal plants from different species. Micropropagation is one of the most used applications of PTC with commercial proposes, mainly in ornamentals (2–7) and medicinal plants (8), although it has also been used in some important crops such as potato, banana (see Chapter 11), herbaceous plants (see Chapter 12), or some forest tree species (Pinus, Eucalyptus, Cedrela, etc., see Chapter 10). There are three ways by which micropropagation can be achieved; these are enhancing axillary bud breaking, production of adventitious buds directly or indirectly via callus, and somatic embryogenesis directly or indirectly on explants (9, 10). Culture conditions, mainly nitrogen source, light regime, temperature, and the container’s atmosphere can play critical roles in favoring bud development in in vitro plants (11–15). Although the propagation protocols for a number of plant species were developed in the 1960s, transition of in vitro to ex vitro conditions even now frequently represents a bottleneck step. Therefore, successful commercial propagation protocols also require procedures for the establishment of plants to field conditions in addition to the efficient multiplication of plantlets (see Chapters 10 and 11). The massive production of embryos, and their later development into entire plants, can also provide a methodology for the propagation of selected materials (see Chapter 14).

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4. Genetic Improvement Genetic improvement in crops is mainly used to produce resistant plants or plants with high phenotypic or organoleptic qualities. Microspore and anther culture (see Chapters 13 and 17) is one of the PTC applications that allows for the regeneration of haploid plants exhibiting unique alleles in just one set of chromosomes. When these haploid plants are treated with the alkaloid colchicine, double-haploid plants with homozygous sets of chromosomes are produced. This phenomenon is used for the generation of isogenic or homozygous lines in one generation in comparison with 5–10 cycles of autofecundation that usually take using the traditional breeding techniques. Furthermore, it is possible to fix hybrid characteristics from parental crosses faster than through the backcrosses usually employed by conventional methods. Hybrid plants from partially sexual compatible parental species (interspecific crosses) that do not occur naturally can be produced by rescuing and culturing in vitro the hybrid embryos before seed abortion (see Chapter 18). Alternatively, it is possible to generate interspecific or even intergeneric hybrids between sexually incompatible plants through somatic fusion using two parental protoplast sources. However, very often these somatic hybrids are unfertile, which prevent their further utilization in breeding programs.

5. Genetic Engineering PTC in combination with recombinant molecular biology techniques have been exploited to introduce and integrate foreign genes from any source (microorganisms, plants, or animals) into the plant genome with the aim of conferring a new characteristic to the transformed or transgenic plant. This process called genetic transformation is carried out by biological or physical methods, the most common being through the infection with Agrobacterium tumefaciens and by microparticle bombardment (biolistic) (see Chapters 27 and 28). By using this technology, different important crops such as corn, cotton, and soybean, among others, have been manipulated to improve their resistance/tolerance to pests, herbicides, or diseases caused by virus, and more recently, production of transgenic corn resistant to drought has been achieved, opening new perspectives for increasing the food production worldwide. Millions of hectares of genetically modified crops are currently under culture in the USA, Argentina, Brazil, Canada, and China, and to a lesser extent in countries such as Paraguay, Mexico, and India, among others.

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There is a great concern regarding the possibility of genetic contamination of wild species from transgenic crops. Since the ecological impact of this type of genetic contamination is still unpredictable, some approaches have been developed to reduce or to eliminate this risk; that is the case of organelle genetic transformation (see Chapter 29). Undoubtedly, plant genetic transformation has been also a key tool for basic studies in Plant Biology. Regulation of gene expression analysis in plant tissues and organs, and the study of gene function are some of examples of applications of genetic transformation.

6. Preservation and Conservation of Plant Germplasm

7. Epigenetics in the Process of Development and In Vitro Culture

Plant genetic resources are of fundamental importance, since they are the primary sources of genetic variability for breeding and crop improvement programs. In general, germplasm from sexually propagated species are conserved in the form of seeds maintained in dry environments and at low temperatures for long time. However, germplasm from species that are usually propagated through vegetative methods or that produce recalcitrant seeds implies that tubers, rhizomes or some vegetative organs must be conserved. This is not an easy task, since very often the volume of vegetative material that should be handled represents a problem involving more space and higher expenses in comparison with conservation of seeds. Furthermore, vegetative organs must be preserved under specific conditions for each plant species. PTC, under minimum growth or through cryopreservation, has been used for plant germplasm conservation (see Chapters 7 and 16). Institutions such as the International Potato Center in Peru or the IPK Gatersleben, Genebank Department, Foundation Leibniz, Institute of Plant Genetics and Crop Plant Research (IPK) in Germany are currently applying these systems as an alternative for germplasm conservation. Since plant tissue cultures are under aseptic conditions, this can allow the exchange of germplasm around the world without quarantine.

In vitro cultures represent an advantageous system for the study of different processes in the cell. Conditions can be strictly controlled allowing monitoring the effects of a single factor on a given process. Elicitation of secondary metabolism in cell cultures has been used for many years to turn on the genes and biosynthetic enzymes

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involved in the biosynthesis of secondary compounds (see Chapter 21). Cell mechanisms for removing metals (see Chapter 20), salinity, or drought among others can be analyzed without having the interference of tissue organization. Furthermore, in vitro cultures submitted to morphogenetic conditions provide an optimum system for the study of the biochemical and molecular aspects associated with plant differentiation (see Chapters 10 and 14). In general, specific foreign genes encoding specific characteristics have been manipulated and transferred by genetic transformation to plant species; however, new strategies involving genetic transformation with microRNAs have opened new possibilities for crop improvement (see Chapter 23). Sometimes, plants produced in in vitro induce variation in their morphology, growth index, productivity, etc. There are some indications that variation in DNA methylation patterns seems to be much more frequent and in some cases it has been directly implicated in phenotypic variation (16). To understand the variation in PTC, as well as different phenotypes produced by cultured cells, the analysis of epigenetic status of the cultures is crucial for the understanding of this phenomenon. An update on the detection of epigenetic variation in plant cell cultures is provided (Chapters 22 and 25), as well the description of a powerful technique to determinate the histone methylation is described (Chapter 24).

8. Future Perspectives Plant cell cultures have turned into an invaluable tool to plant scientists, and today, in vitro culture techniques are standard procedures in most laboratories around the world. This technology goes beyond academic laboratories. Companies around the world are using plant tissue culture techniques for the massive propagation of plants. The development of genomics, proteomics, metabolomics, and more recently epigenetics has allowed the advances in different techniques relates to PTC and in the understanding of basic biological process. These approaches, with no doubt, will accelerate the discovery, isolation ,and characterization of genes conferring new agronomic traits to crops. Between the most important challengers ahead are the increments in yields in commercial important crops, the production of better raw material for biofuel production, the increment in vitamins and nutritional proteins in food crops, as well as the generation of plants capable of to absorb contaminants from the environment. In order to achieve this goal, we need to produce resistant crops against the major diseases pathogens agents, as well as to abiotic stress. Since many of these traits are multigenic characters, the introduction of several genes in each transformation event will be important. The metabolic engineering techniques and

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the uses of PTC must provide new raw materials for the production of bioethanol and biodiesel. The development of the techniques will keep cell culture scientists busy for many years. References 1. Thorpe TA (1990) The current status of plant tissue culture. In: Bhojwani SS (ed) Plant tissue culture: applications and limitations, vol 19, Developments in crop science. Elsevier, Amsterdam, pp 1–33 2. Conger BV (1980) Cloning agricultural plants via in vitro techniques. CRC, Boca Raton, FL 3. George EF (1996) Plant propagation by tissue culture. Part 2. Exegetics, Edington 4. Debergh PC, Zimmerman RH (1993) Micropropagation. Technology and application. Kluwer, Dordrecht 5. Herman EB (1991) Recent advances in plant tissue culture. Regeneration, micropropagation and media 1988-1991. Agritech, Shrub Oak, NY 6. Herman EB (1995) Recent advances in plant tissue culture III. Regeneration and micropropagation: techniques, systems and media 1991-1995. Agritech, Shrub Oak, NY 7. Kyte L, Kleyn J (1996) Plant from test tubes. An introduction to micropropagation. Timber, Portland, OR 8. Debnath M, Malik CP, Bisen PS (2006) Micropropagation: a tool for the production of high quality plant-based medicines. Curr Pharm Biotechnol 7:33–49

9. Murashige T (1974) Plant propagation through tissue cultures. Annu Rev Plant Physiol 25:135–166 10. George EF (1993) Plant propagation and micropropagation. In: George EF (ed) Plant propagation by tissue culture. Part 1. Exegetics, Edington, pp 37–66 11. Hazarika BN (2006) Morpho-physiological disorders in in vitro culture of plants. Sci Hortic 108:105–120 12. Huang C, Chen C (2005) Physical properties of culture vessels for plant tissue culture. Biosyst Eng 91:501–511 13. Chen C (2004) Humidity in plant tissue culture vessels. Biosyst Eng 88:231–241 14. Zobayed SMA, Afreen F, Xiao Y et al (2004) Recent advancement in research on photoautotrophic micropropagation using large culture vessels with forced ventilation. In Vitro Cell Dev Biol Plant 40:450–458 15. Lowe KC, Anthony P, Power JB et al (2003) Novel approaches for regulating gas supply to plant systems in vitro: application and benefits of artificial gas carriers. In Vitro Cell Dev Biol Plant 39:557–566 16. Miguel C, Marum L (2011) An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond. J Exp Bot 62: 3713–3725

Chapter 2 History of Plant Tissue Culture Trevor Thorpe Abstract Plant tissue culture, or the aseptic culture of cells, tissues, organs, and their components under defined physical and chemical conditions in vitro, is an important tool in both basic and applied studies as well as in commercial application. It owes its origin to the ideas of the German scientist, Haberlandt, at the beginning of the twentieth century. The early studies led to root cultures, embryo cultures, and the first true callus/tissue cultures. The period between the 1940s and the 1960s was marked by the development of new techniques and the improvement of those that were already in use. It was the availability of these techniques that led to the application of tissue culture to five broad areas, namely, cell behavior (including cytology, nutrition, metabolism, morphogenesis, embryogenesis, and pathology), plant modification and improvement, pathogen-free plants and germplasm storage, clonal propagation, and product (mainly secondary metabolite) formation, starting in the mid-1960s. The 1990s saw continued expansion in the application of the in vitro technologies to an increasing number of plant species. Cell cultures have remained an important tool in the study of basic areas of plant biology and biochemistry and have assumed major significance in studies in molecular biology and agricultural biotechnology in the twenty-first century. The historical development of these in vitro technologies and their applications is the focus of this chapter. Key words: Cell behavior, Cell suspensions, Clonal propagation, Organogenesis, Plantlet regeneration, Plant transformation, Protoplasts’ somatic embryogenesis, Vector-dependent/independent gene transfer

1. Introduction Plant tissue culture, also referred to as cell, in vitro, axenic, or sterile culture, is an important tool in both basic and applied studies, as well as in commercial application (1). Plant tissue culture is the aseptic culture of cells, tissues, organs, and their components under defined physical and chemical conditions in vitro. The theoretical basis for plant tissue culture was proposed by Gottlieb Haberlandt in his address to the German Academy of Science in 1902 on his experiments on the culture of single cells (2). He opined that, to his knowledge, no systematically organized attempts to culture-isolated

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_2, © Springer Science+Business Media, LLC 2012

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vegetative cells from higher plants have been made. Yet the results of such culture experiments should give some interesting insight to the properties and potentialities that the cell, as an elementary organism, possesses. Moreover, it would provide information about the interrelationships and complementary influences to which cells within a multicellular whole organism are exposed (from the English translation (3)). He experimented with isolated photosynthetic leaf cells and other functionally differenced cells and was unsuccessful, but nevertheless he predicted that one could successfully cultivate artificial embryos from vegetative cells. He, thus, clearly established the concept of totipotency, and further indicated that the technique of cultivating isolated plant cells in nutrient solution permits the investigation of important problems from a new experimental approach. On the basis of that 1902 address and his pioneering experimentation before and later, Haberlandt is justifiably recognized as the father of plant tissue culture. Other studies led to the culture of isolated root tips (4, 5). This approach of using explants with meristematic cells produced the successful and indefinite culture of tomato root tips (6). Further work allowed for root culture on a completely defined medium. Such root cultures were used initially for viral studies and later as a major tool for physiological studies (7). Success was also achieved with bud cultures (8, 9). Embryo culture also had its beginning early in the first decade of the last century with barley embryos (10). This was followed by the successful rescue of embryos from nonviable seeds of a cross between Linum perenne ↔ Linum austriacum (11), and for full embryo development in some early ripening species of fruit trees (12), thus providing one of the earliest applications of in vitro culture. The phenomenon of precocious germination was also encountered (13). The first true plant tissue cultures were obtained by Gautheret (14, 15) from cambial tissue of Acer pseudoplatanus. He also obtained success with similar explants of Ulmus campestre, Robinia pseudoacacia, and Salix capraea using agar-solidified medium of Knop’s solution, glucose, and cysteine hydrochloride. Later, the availability of indole acetic acid and the addition of B vitamins allowed for the more or less simultaneous demonstrations with carrot root tissues (16, 17), and with tumor tissue of a Nicotiana glauca Nicotiana langsdorffii hybrid (18), which did not require auxin, that tissues could be continuously grown in culture and even made to differentiate roots and shoots (19, 20). However, all of the initial explants used by these pioneers included meristematic tissue. Nevertheless, these findings set the stage for the dramatic increase in the use of in vitro cultures in the subsequent decades. Greater detail on the early pioneering events in plant tissue culture could be found in White (21), Bhojwani and Razdan (22), and Gautheret (23). This current article is based on an earlier review by the author (24) (used with permission from Elsevier).

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The l940s, 1950s, and 1960s proved an exciting time for the development of new techniques and the improvement of those already available. The application of coconut water (often incorrectly referred to as coconut milk) allowed for the culture of young embryos (25) and other recalcitrant tissues, including monocots. Callus cultures of numerous species, including a variety of woody and herbaceous dicots and gymnosperms, as well as crown-gall tissues, were established as well (23). It was recognized at that time that cells in culture underwent a variety of changes, including loss of sensitivity to applied auxin or habituation (26, 27), as well as variability of meristems formed from callus (27, 28). Nevertheless, it was during that period that most of the in vitro techniques used today were largely developed. Studies by Skoog and Tsui (29) showed that the addition of adenine and high levels of phosphate allowed nonmeristematic pith tissues to be cultured and produced shoots and roots, but only in the presence of vascular tissue. Further studies using nucleic acids led to the discovery of the first cytokinin (kinetin), as the breakdown product of herring sperm DNA (30). The availability of kinetin further increased the number of species that could be cultured indefinitely, but, perhaps most importantly, led to the recognition that the exogenous balance of auxin and kinetin in the medium influenced the morphogenic fate of tobacco callus (31). A relative high level of auxin to kinetin favored rooting, and the reverse led to shoot formation and intermediate levels to the proliferation of callus or wound parenchyma tissue. This morphogenic model has been shown to operate in numerous species (32). Native cytokinins were subsequently discovered in several tissues, including coconut water (33). The formation of bipolar somatic embryos (carrot) was first reported independently by Reinert (34, 35) and Steward (36) in addition to the formation of unipolar shoot buds and roots. The culture of single cells (and small cell clumps) was achieved by shaking callus cultures of Tagetes erecta and tobacco, and subsequently placing them on filter paper resting on well-established callus, giving rise to the so-called nurse culture (37, 38). Later, single cells could be grown in the medium in which tissues had already been grown (i.e., conditioned medium) (39). As well, single cells incorporated in a 1-mm layer of solidified medium formed some cell colonies (40). This technique is widely used for cloning cells and in protoplast culture (22). Finally, in 1959, success was achieved in the culture of mechanically isolated mature differentiated mesophyll cells of Macleaya cordata (41), and later in the induction of somatic embryos from the callus (42). The first largescale culture of plant cells was obtained from cell suspensions of

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Ginkgo, holly, Lolium, and rose in simple sparged 20-L carboys (43). The utilization of coconut water as an additive to fresh medium, instead of using conditioned medium, finally led to realization of Haberlandt’s dream of producing a whole plant (tobacco) from a single cell by Vasil and Hildebrandt (44), thus demonstrating the totipotency of plant cells. The earliest nutrient media used for growing plant tissues in vitro were based on the nutrient formulations for whole plants, for which there were many (21); but Knop’s solution and that of Uspenski and Uspenskia were used the most, and provided less than 200 mg/L of total salts. Based on studies with carrot and Virginia creeper tissues, the concentration of salts was increased twofold (45), and was further increased ca. 4 g/L, based on the work with Jerusalem artichoke (46). However, these changes did not provide optimum growth for tissues, and complex addenda, such as yeast extract, protein hydrolysates, and coconut water, were frequently required. In a different approach, based on an examination of the ash of tobacco callus, Murashige and Skoog (MS) (47) developed a new medium. The concentration of some salts was 25 times that of Knop’s solution. In particular, the levels of NO3− and NH4+ were very high and the arrays of micronutrients were increased. MS formulation allowed for a further increase in the number of plant species that could be cultured, many of them using only a defined medium consisting of macro- and micronutrients, a carbon source, reduced N, B vitamins, and growth regulators (48). The MS salt formulation is now the most widely used nutrient medium in plant tissue culture. Plantlets were successfully produced by culturing shoot tips with a couple of primordia of Lupinus and Tropaeoluni (9), but the importance of this finding was not recognized until later when this approach to obtain virus-free orchids, demonstrated its potential for clonal propagation (49). The potential was rapidly exploited, particularly with ornamentals (50). Early studies had shown that cultured root tips were free of viruses (51). It was later observed that the virus titer in the shoot meristem was very low (52). This was confirmed when virus-free Dahlia plants were obtained from infected plants by culturing their shoot tips (53). Virus elimination was possible because vascular tissues, within which the viruses move, do not extend into the root or shoot apex. The method was further refined (54), and is now routinely used. Techniques for in vitro culture of floral and seed parts were developed during this period (55). The first attempts at ovary culture yielded limited growth of the ovaries accompanied by rooting of pedicels in several species (56). Compared to studies with embryos, successful ovule culture is very limited. Studies with both ovaries and ovules have been geared mainly to an understanding of factors regulating embryo and fruit development (56). The first continuously growing tissue cultures from an endosperm were

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from immature maize (57). Plantlet regeneration via organogenesis was later achieved in Exocarpus cupressiformis (58). In vitro pollination and fertilization was pioneered using Papaver somniferum (59). The approach involves culturing excised ovules and pollen grains together in the same medium and has been used to produce interspecific and intergeneric hybrids (60). Earlier, cell colonies were obtained from Ginkgo pollen grains in culture (61), and haploid callus was obtained from whole anthers of Tradescantia reflexa (62). However, it was the finding of Guha and Maheshwari (63, 64) that haploid plants could be obtained from cultured anthers of Datura innoxia that opened the new area of androgenesis. Haploid plants of tobacco were also obtained (65), thus confirming the totipotency of pollen grains. Plant protoplasts or cells without cell walls were first mechanically isolated from plasmolysed tissues well over 100 years ago, and the first fusion was achieved in 1909 (23). Nevertheless, this remained an unexplored technology until the use of a fungal cellulase by Cocking (66) ushered in a new era. The commercial availability of cell wall-degrading enzymes led to their wide use and the development of protoplast technology in the 1970s. The first demonstration of the totipotency of protoplasts was by Takebe et al. (67), who obtained tobacco plants from mesophyll protoplasts. This was followed by the regeneration of the first interspecific hybrid plants (N. glauca ↔ N. langsdorffii) (68). Braun (69) showed that in sunflower Agrobacterium tumefaciens could induce tumors not only at the inoculated sites, but also at distant points. These secondary tumors were free of bacteria and their cells could be cultured without auxin (70). Further experiments showed that crown gall tissues, free of bacteria, contained a tumor-inducing principle (TIP), which was probably a macromolecule (71). The nature of the TIP was worked out in the 1970s (72), but Braun’s work served as the foundation for Agrobacteriumbased transformation. It should also be noted that the finding by Ledoux (73) that plant cells could take up and integrate DNA remained controversial for more than a decade.

3. The Recent Past Based on the availability of the various in vitro techniques discussed in Subheading 2, it is not surprising that, starting in the mid-l960s, there was a dramatic increase in their application to various problems in basic biology, agriculture, horticulture, and forestry through the 1970s and 1980s. These applications can be divided conveniently into five broad areas, namely: (1) cell behavior, (2) plant modification and improvement, (3) pathogen-free plants and germplasm storage, (4) clonal propagation, and (5) product formation (1).

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Detailed information on the approaches used can be gleaned from Bhojwani and Razdan (22), Vasil (74), and Vasil and Thorpe (75), among several sources. 3.1. Cell Behavior

Included under this heading are studies dealing with cytology, nutrition, primary, and secondary metabolism, as well as morphogenesis and pathology of cultured tissues (1). Studies on the structure and physiology of quiescent cells in explants, changes in cell structure associated with the induction of division in these explants and the characteristics of developing callus, and cultured cells and protoplasts have been carried out using light and electron microscopy (76–79). Nuclear cytology studies have shown that endoreduplication, endomitosis, and nuclear fragmentation are common features of cultured cells (80, 81). Nutrition was the earliest aspect of plant tissue culture investigated, as indicated earlier. Progress has been made in the culture of photoautotrophic cells (82, 83). In vitro cultures, particularly cell suspensions, have become very useful in the study of both primary and secondary metabolism (84). In addition to providing protoplasts from which intact and viable organelles were obtained for study (e.g., vacuoles) (85), cell suspensions have been used to study the regulation of inorganic nitrogen and sulfur assimilation (86), carbohydrate metabolism (87), and photosynthetic carbon metabolism (88, 89), thus clearly showing the usefulness of cell cultures for elucidating pathway activity. Most of the work on secondary metabolism was related to the potential of cultured cells to form commercial products, but has also yielded basic biochemical information (90, 91). Morphogenesis or the origin of form is an area of research with which tissue culture has long been associated, and one to which tissue culture has made significant contributions both in terms of fundamental knowledge and application (1). Xylogenesis or tracheary element formation has been used to study cytodifferentiation (92–94). In particular, the optimization of the Zinnia mesophyll single-cell system has dramatically improved our knowledge of this process. The classical findings of Skoog and Miller (31) on the hormonal balance for organogenesis have continued to influence research on this topic: a concept supported more recently by transformation of cells with appropriately modified Agrobacterium T-DNA (95, 96). However, it is clear from the literature that several additional factors, including other growth active substances, interact with auxin and cytokinin to bring about de novo organogenesis (97). In addition to bulky explants, such as cotyledons, hypocotyls, and callus (97), thin (superficial) cell layers (98, 99) have been used in traditional morphogenic studies, as well as to produce de novo organs and plantlets in hundreds of plant species (50, 100). As well, physiological and biochemical studies on organogenesis have been carried out (97, 101, 102).

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The third area of morphogenesis, somatic embryogenesis, also developed in this period with over 130 species reported to form the bipolar structures by the early l980s (103, 104). Successful culture was achieved with cereals, grasses, legumes, and conifers, previously considered to be recalcitrant groups. The development of a single cell to embryo system in carrot (105) has allowed for an in depth study of the process. Cell cultures have continued to play an important role in the study of plant–microbe interaction not only in tumorigenesis (106), but also in the biochemistry of virus multiplication (107), phytotoxin action (108), and disease resistance, particularly as affected by phytoalexins (109). Without doubt, the most important studies in this area dealt with Agrobacteria and, although aimed mainly at plant improvement (see Subheading 3.2), provided good fundamental information (96). 3.2. Plant Modification and Improvement

During this period, in vitro methods were increasingly used as an adjunct to traditional breeding methods for the modification and improvement of plants. The technique of controlled in vitro pollination on the stigma, placenta, or ovule has been used for the production of interspecific and intergeneric hybrids, overcoming sexual self-incompatibility, and the induction of haploid plants (109). Embryo, ovary, and ovule cultures have been used in overcoming embryo inviability, monoploid production in barley, and seed dormancy and related problems (110–112). In particular, embryo rescue has played a most important role in producing interspecific and intergeneric hybrids (113). By the early 1980s, androgenesis had been reported in some 171 species, many of which were important crop plants (114). Gynogenesis was reported in some 15 species, in some of which androgenesis was not successful (115). The value of these haploids was that they could be used to detect mutations and for the recovery of unique recombinants because there is no masking of recessive alleles. As well, the production of double haploids allowed for hybrid production and their integration into breeding programs. Cell cultures have also played an important role in plant modification and improvement, as they offer advantages for isolation of variants (116). Although tissue culture produced variants that have been known since the 1940s (e.g., habituation), it was only in the 1970s that attempts were made to utilize them for plant improvement. This somaclonal variation is dependent on the natural variation in a population of cells, either preexisting or culture induced, and is usually observed in regenerated plantlets (117). The variation may be genetic or epigenetic and is not simple in origin (118, 119). The changes in the regenerated plantlets have potential agricultural and horticultural significance, but this potential has not yet been realized. It has also been possible to produce a wide spectrum of mutant cells in culture (120). These include cells showing

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biochemical differences, antibiotic, herbicide, and stress resistance. In addition, auxotrophs, autotrophs, and those with altered developmental systems have been selected in culture; usually, the application of the selective agent in the presence of a mutagen is required. However, in only a few cases has it been possible to regenerate plants with the desired traits (e.g., herbicide-resistant tobacco) (121) and methyl tryptophan-resistant Datura innoxia (122). By 1985, nearly 100 species of angiosperms could be regenerated from protoplasts (123). The ability to fuse plant protoplasts by chemical (e.g., with polyethylene glycol (PEG)) and physical means (e.g., electrofusion) allowed for the production of somatic hybrid plants, the major problem being the ability to regenerate plants from the hybrid cells (124, 125). Protoplast fusion has been used to produce unique nuclear-cytoplasmic combinations. In one such example, Brassica campestris chloroplasts coding for atrazine resistance (obtained from protoplasts) were transferred into B. napus protoplasts with Raphanus sativus cytoplasm (which confers cytoplasmic male sterility from its mitochondria). The selected plants that contained B. napus nuclei, chloroplasts from B. campestris, and mitochondria from R. sativus had the desired traits in a B. napus phenotype, and could be used for hybrid seed production (126). Unfortunately, only a few such examples exist to date. Genetic modification of plants has been achieved by direct DNA transfer via vector-independent and vector-dependent means since the early l980s. Vector-independent methods with protoplasts include electroporation (127), liposome fusion (128), and microinjection (129), as well as high-velocity microprojectile bombardment (biolistics) (130). This latter method can be executed with cells, tissues, and organs. The use of Agrobacterium in vectormediated transfer has progressed very rapidly since the first reports of stable transformation (131, 132). Although the early transformations utilized protoplasts, regenerable organs, such as leaves, stems, and roots, have been subsequently used (133, 134). Much of the research activity utilizing these tools has focused on engineering important agricultural traits for the control of insects, weeds, and plant diseases. 3.3. Pathogen-Free Plants and Germplasm Storage

Although these two uses of in vitro technology may appear unrelated, a major use of pathogen-free plants is for germplasm storage and the movement of living material across international borders (1). The ability to rid plants of viruses, bacteria, and fungi by culturing meristem tips has been widely used since the 1960s. The approach is particularly needed for virus-infected material because bactericidal and fungicidal agents cannot be used successfully in ridding plants of bacteria and fungi (22). Meristem-tip culture is often coupled with thermotherapy or chemotherapy for virus eradication (135).

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Traditionally, germplasm has been maintained as seed, but the ability to regenerate whole plants from somatic and gametic cells and shoot apices has led to their use for storage (22, 135). Three in vitro approaches have been developed, namely, use of growthretarding compounds (e.g., maleic hydrazide, B995, and abscisic acid [ABA]) (136), low-nonfreezing temperatures (1–9°C) (22), and cryopreservation (135). In this last approach, cell suspensions, shoot apices, asexual embryos, and young plantlets, after treatment with a cryoprotectant, are frozen and stored at the temperature of liquid nitrogen (ca. −196°C) (135, 137). 3.4. Clonal Propagation

The use of tissue culture technology for the vegetative propagation of plants is the most widely used application of the technology. It has been used with all classes of plants (138, 139), although some problems still need to be resolved (e.g., hyperhydricity, aberrant plants). There are three ways by which micropropagation can be achieved. These are enhancing axillary bud breaking, production of adventitious buds directly or indirectly via callus, and somatic embryogenesis directly or indirectly on explants (50, 138). Axillary bud breaking produces the smallest number of plantlets, but they are generally genetically true to type, whereas somatic embryogenesis has the potential to produce the greatest number of plantlets, but is induced in the lowest number of plant species. Commercially, numerous ornamentals are produced, mainly via axillary bud breaking (140). As well, there are many lab-scale protocols for other classes of plants, including field and vegetable crops, fruit, plantation, and forest trees, but cost of production is often a limiting factor in their use commercially (141).

3.5. Product Formation

Higher plants produce a large number of diverse organic chemicals, which are of pharmaceutical and industrial interest. The first attempt at the large-scale culture of plant cells for the production of pharmaceuticals took place in the 1950s at the Charles Pfizer Co. The failure of this effort limited research in this area in the USA, but work elsewhere in Germany and Japan in particular, led to the development; hence, by 1978, the industrial application of cell cultures was considered feasible (142). Furthermore, by 1987, there were 30 cell culture systems that were better producers of secondary metabolites than the respective plants (143). Unfortunately, many of the economically important plant products are either not formed in sufficiently large quantities or not at all by plant cell cultures. Different approaches have been taken to enhance yields of secondary metabolites. These include cell cloning and the repeated selection of high-yielding strains from heterogeneous cell populations (142, 144) and by using enzyme-linked immunosorbent assay (ELISA) and radioimmunoassay techniques (145). Another approach involves selection of mutant cell lines that overproduce the desired product (146). As well, both abiotic

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factors—such as ultraviolet (UV) irradiation and exposure to heat or cold and salts of heavy metals—and biotic elicitors of plant and microbial origin have been shown to enhance secondary product formation (147, 148). Lastly, the use of immobilized cell technology has also been examined (149, 150). Central to the success of producing biologically active substances commercially is the capacity to grow cells on a large scale. This is being achieved using stirred tank reactor systems and a range of air-driven reactors (141). For many systems, a two-stage (or two-phase) culture process has been tried (151, 152). In the first stage, rapid cell growth and biomass accumulation are emphasized, whereas the second stage concentrates on product synthesis with minimal cell division or growth. However, by 1987, the naphthoquinone, shikonin, was the only commercially produced secondary metabolite by cell cultures (153).

4. The Present During the 1990s, continued expansion in the application of in vitro technologies to an increasing number of plant species was observed. Tissue culture techniques are being used with all types of plants, including cereals and grasses (154), legumes (155), vegetable crops (156), potato (157), other root and tuber crops (158), oilseeds (159), temperate (160) and tropical (161) fruits, plantation crops (162), forest trees (163), and, of course, ornamentals (164). As can be seen from these articles, the application of in vitro cell technology went well beyond micropropagation, and embraced all the in vitro approaches that were relevant or possible for the particular species, and the problem(s) being addressed. However, only limited success has been achieved in exploiting somaclonal variation (165) or in the regeneration of useful plantlets from mutant cells (166); also, the early promise of protoplast technology has remained largely unfulfilled (167). Substantial progress has been made in extending cryopreservation technology for germplasm storage (168) and in artificial seed technology (169). Some novel approaches for culturing cells, such as on rafts, membranes, and glass rods, as well as manipulation of the culture environment by use of nonionic surfactants have been successfully developed (170). Cell cultures have remained an important tool in the study of plant biology. Thus, progress is being made in cell biology, for example, in studies of the cytoskeleton (171), on chromosomal changes in cultured cells (172), and in cell-cycle studies (173, 174). Better physiological and biochemical tools have allowed for a reexamination of neoplastic growth in cell cultures during habituation and hyperhydricity, and to relate it to possible cancerous growth in plants (175). Cell cultures have remained an extremely important

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tool in the study of primary metabolism, for example the use of cell suspensions to develop in vitro transcription systems (176) or the regulation of carbohydrate metabolism in transgenics (177). The development of medicinal plant cell-culture techniques has led to the identification of more than 80 enzymes of alkaloid biosynthesis (reviewed in ref. 178). Similar information arising from the use of cell cultures for molecular and biochemical studies on other areas of secondary metabolism is generating research activity on metabolic engineering of plant secondary metabolite production (179). Cell cultures remain an important tool in the study of morphogenesis, even though the present use of developmental mutants, particularly of Arabidopsis, is adding valuable information on plant development (see ref. 180). Molecular, physiological, and biochemical studies have allowed for an in depth understanding of cytodifferentiation, mainly tracheary element formation (181), organogenesis (182, 183), and somatic embryogenesis (184–186). Advances in molecular biology are allowing for the genetic engineering of plants through the precise insertion of foreign genes from diverse biological systems. Three major breakthroughs have played major roles in the development of this transformation technology (187). These are the development of shuttle vectors for harnessing the natural gene transfer capability of Agrobacterium (188), the methods to use these vectors for the direct transformation of regenerable explants obtained from plant organs (189), and the development of selectable markers (190). For species not amenable to Agrobacterium-mediated transformation, physical, chemical, and mechanical means are used to get the DNA into the cells. With these latter approaches, particularly biolistics (191), it has become possible to transform virtually any plant species and genotype. The initial wave of research in plant biotechnology has been driven mainly by the seed and agrochemical industries, and has concentrated on the agronomic traits of direct relevance to these industries, namely, the control of insects, weeds, and plant diseases (192). At present, over 100 species of plants have been genetically engineered, including nearly all the major dicotyledonous crops and an increasing number of monocotyledonous ones, as well as some woody plants. Current research is leading to routine gene transfer systems for all-important crops, for example the production of golden rice (193). In addition, technical improvements are further increasing transformation efficiency, extending transformation to elite commercial germplasm, and lowering transgenic plant production costs. The next wave in agricultural biotechnology is already in progress with biotechnological applications of interest to the food processing, specially chemical, and pharmaceutical industries. The current emphasis and importance of plant biotechnology can be gleamed from the last three International Congresses on

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Plant Tissue and Cell Culture and Biotechnology held in Israel in June 1998, in the USA in June 2002, and in China in August 2006. The theme of the Israeli Congress was Plant Biotechnology and In Vitro Biology in the 21st Century; the theme of the 2002 Congress was Plant Biotechnology 2002 and Beyond, while the theme of the 2006 Congress was Biotechnology and Sustainable Agriculture 2006 and Beyond. The proceedings for these three congresses (194–196) were developed through scientific programs that focused on the most important developments, both basic and applied, in the areas of plant tissue culture and molecular biology and their impact on plant improvement and biotechnology. They clearly show where tissue culture is today and where it is heading (i.e., as an equal partner with molecular biology) as a tool in basic plant biology and in various areas of application. In fact, progress in applied plant biotechnology is fully matching and is without doubt stimulating fundamental scientific progress, which remains the best hope for achieving sustainable and environmentally stable agriculture (197). Indeed, the advancements made in the last 100 years with in vitro technology have gone well beyond what Haberlandt and other pioneers could have imagined. References 1. Thorpe TA (1990) The current status of plant tissue culture. In: Bhojwani SS (ed) Plant tissue culture: applications and limitations. Elsevier, Amsterdam, pp 1–33 2. Haberlandt G (1902) Kulturversuche mit isolierten Pflanzenzellen. Sitzungsber. Akad Wiss Wien. Math-Naturwiss Kl Abt J 111: 69–92 3. Krikorian AD, Berquarn DL (1969) Plant cell and tissue cultures: the role of Haberlandt. Botan Rev 35:59–67 4. Kotte W (1922) Kulturversuche mit isolierten Wurzelspitzen. Beitr Allg Bot 2:413–434 5. Robbins WJ (1922) Cultivation of excised root tips and stem tips under sterile conditions. Bot Gaz 73:376–390 6. White PR (1934) Potentially unlimited growth of excised tomato root tips in a liquid medium. Plant Physiol 9:585–600 7. Street HE (1969) Growth in organized and unorganized Systems. In: Steward FC (ed) Plant physiology, vol 5B. Academic, New York, pp 3–224 8. Loo SW (1945) Cultivation of excised stem tips of asparagus in vitro. Am J Bot 32: 13–17 9. Ball E (1946) Development in sterile culture of sterns tips and subjacent regions of Tropaeolum malus L. and of Lupinus albus L. Am J Bot 33:301–318

10. Monnier M (1995) Culture of zygotic embryos. In: Thorpe TA (ed) In vitro embryogenesis in plants. Kluwer, Dordrecht, pp 117–153 11. Laibach F (1929) Ectogenesis in plants. Methods and genetic possibilities of propagating embryos otherwise dying in the seed. J Hered 20(20):1–208 12. Tukey HB (1934) Artificial culture methods for isolated embryos of deciduous fruits. Proc Am Soc Hortic Sci 32:313–322 13. LaRue CD (1936) The growth of plant embryos in culture. Bull Torrey Bot Club 63: 365–382 14. Gautheret RJ (1934) Culture du tissus cambial. CR Hebd Seances Acad Sci 198: 2195–2196 15. Gautheret RJ (1935) Recherches sur la culture des tissus végétaux. Ph.D. Thesis, Paris 16. Gautheret RJ (1939) Sur la possibilité de réaliser la culture indéfinie des tissus de tubercules de carotte. CR Hebd Seances Acad Sci 208:118–120 17. Nobécourt P (1939) Sur la pérennité et l’augmentation de volume des cultures de tissues végétaux. CR Seances Soc Biol Ses Fil 130:1270–1271 18. White PR (1939) Potentially unlimited growth of excised plant callus in an artificial nutrient. Am J Bot 26:59–64

2 19. Nobécourt P (1939) Sur les radicelles naissant des cultures de tissus végétaux. CR Seances Soc Biol Ses Fil 130:1271–1272 20. White PR (1939) Controlled differentiation in a plant tissue culture. Bull Torrey Bot Club 66:507–513 21. White PR (1963) The cultivation of animal and plant cells, 2nd edn. Ronald, New York 22. Bhojwani SS, Razdan MK (1983) Plant tissue culture: theory and practice. development in crop science, vol 5. Elsevier, Amsterdam 23. Gautheret RJ (1985) History of plant tissue and cell culture: a personal account. In: Vasil IK (ed) Cell culture and somatic cell genetics of plants, vol 2. Academic, New York, pp 1–59 24. Thorpe TA (2000) History of plant cell culture. In: Smith RH (ed) Plant tissue culture: techniques and experiments, 2nd edn. Academic, San Diego, pp 1–32, With permission from Elsevier 25. Van Overbeek J, Conklin ME, Blakeslee AF (1941) Factors in coconut milk essential for growth and development of very young Datura embryos. Science 94:350–351 26. Gautheret RJ (1942) Hétéro-auxines et cultures de tissus végétaux. Bull Soc Chim Biol 24:13–41 27. Gautheret RJ (1955) Sur la variabilité des propriétés physiologiques des cultures de tissues végétaux. Rev Gén Bot 62:5–112 28. Nobécourt P (1955) Variations de la morphologie et de la structure de cultures de tissues végétaux. Ber Schweiz Bot Ges 65: 475–480 29. Skoog F, Tsui C (1948) Chemical control of growth and bud formation in tobacco stem segments and callus cultured in vitro. Am J Bot 35:782–787 30. Miller C, Skoog F, Von Saltza MH, Strong FM (1955) Kinetin, a cell division factor from deoxyribonucleic acid. J Am Chem Soc 77: 1392 31. Skoog F, Miller CO (1957) Chemical regulation of growth and organ formation in plant tissue cultures in vitro. Symp Soc Exp Biol 11:118–131 32. Evans DA, Sharp WR, Flick CE (1981) Growth and behavior of cell cultures: embryogenesis and organogenesis. In: Thorpe TA (ed) Plant tissue culture: methods and applications in agriculture. Academic, New York, pp 45–113 33. Letham DS (1974) Regulators of cell division in plant tissues. The cytokinins of coconut milk. Physiol Plant 32:66–70

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34. Reinert J (1958) Utersuchungen die Morphogenese an Gewebekulturen. Ber Dtsch Bot Ges 71:15 35. Reinert J (1959) Uber die Kontrolle der Morphogenese und die Induktion von Adventivembryonen an Gewebekulturen aus Karotten. Planta 53:318–333 36. Steward FC, Mapes MO, Mears K (1958) Growth and organized development of cultured cells. II. Organization in cultures grown from freely suspended cells. Am J Bot 45: 705–708 37. Muir WH, Hildebrandt AC, Riker AJ (1954) Plant tissue cultures produced from single isolated plant cells. Science 119:877–878 38. Muir WH, Hildebrandt AC, Riker AJ (1958) The preparation, isolation and growth in culture of single cells from higher plants. Am J Bot 45:585–597 39. Jones LE, Hildebrandt AC, Riker AJ et al (1960) Growth of somatic tobacco cells in microculture. Am J Bot 47:468–475 40. Bergmann L (1959) A new technique for isolating and cloning cells of higher plants. Nature 184:648–649 41. Kohlenbach HW (1959) Streckungs-und Teilungswachstum isolierter Mesophyllzellen von Macleaya cordata (Wild.) R. Br. Naturwissenschaften 46:116–117 42. Kohlenbach HW (1966) Die Entwicklungspotenzen explantienter und isolierter Daueizellen. I. Das Strechungs-und Teilungswachstum isolierter Mesophyllzellen von Macleaya cordata. Z Pflanzenphysiol 55: 142–157 43. Tulecke W, Nickell LG (1959) Production of large amounts of plant tissue by submerged culture. Science 130:863–864 44. Vasil V, Hildebrandt AC (1965) Differentiation of tobacco plants from single, isolated cells in micro cultures. Science 150:889–892 45. Heller R (1953) Recherches sur la nutrition minerale des tissus végétaux cultivé in vitro. Ann Sci Nat Bot Biol Veg 14:1–223 46. Nitsch JP, Nitsch C (1956) Auxin-dependent growth of. excised Helianthus tuberosus tissues. Am J Bot 43:839–851 47. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15: 473–497 48. Gamborg OL, Murashige T, Thorpe TA et al (1976) Plant tissue culture media. In Vitro 12:473–478 49. Morel G (1960) Producing virus-free cymbidium. Am Orchid Soc Bull 29:495–497

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50. Murashige T (1974) Plant propagation through tissue culture. Annu Rev Plant Physiol 25:135–166 51. White PR (1934) Multiplication of the viruses of tobacco and Aucuba mosaics in growing excised tomato root tips. Phytopathology 24:1003–1011 52. Limasset P, Cornuet P (1949) Recherche du virus de la mosaïque du tabac dans les méristèmes des plantes infectées. CR Hebd Seances Acad Sci 228:1971–1972 53. Morel G, Martin C (1952) Guérison de dahlias atteints d’une maladie á virus. CR Hebd Seances Acad Sci 235:1324–1325 54. Quack F (1961) Heat treatment and substances inhibiting virus multiplication in meristem culture to obtain virus-free plants. Adv Hortic Sci Their Appl Proc Int Hortic Congr 15th 1958 1:144–148 55. LaRue CD (1942) The rooting of flowers in culture. Bull Torrey Bot Club 69:332–341 56. Rangan TS (1982) Ovary, ovule and nucellus culture. In: Johri BM (ed) Experimental embryology of vascular plants. Springer, Berlin, pp 105–129 57. LaRue CD (1949) Culture of the endosperm of maize. Am J Bot 36:798 58. Johri BM, Bhojwani SS (1965) Growth responses of mature endosperm in cultures. Nature 208:1345–1347 59. Kanta K, Rangaswamy NS, Maheshwari P (1962) Test-tube fertilization in flowering plants. Nature 194:1214–1217 60. Zenkteler M, Misiura E, Guzowska I (1975) Studies on obtaining hybrid embryos in test tubes. In: Mohan Ram HY, Shaw JJ, Shaw CK (eds) Form, structure and function in plants. Sarita Prakashan, Meerut, India, pp 180–187 61. Tulecke W (1953) A tissue derived from the pollen of Ginkgo biloba. Science 117: 599–600 62. Yamada T, Shoji T, Sinoto Y (1963) Formation of calli and free cells in a tissue culture of Tradescantia reflexa. Bot Mag 76:332–339 63. Guha S, Maheshwari SC (1964) In vitro production of embryos from anthers of Datura. Nature 204:497 64. Guha S, Maheshwari SC (1966) Cell division and differentiation of embryos in the pollen grains of Datura in vitro. Nature 212:97–98 65. Bourgin JP, Nitch JP (1967) Obtention de Nicotiana haploides à partir d’étamines cultivées in vitro. Ann Physiol Vég 9:377–382 66. Cocking EC (1960) A method for the isolation of plant protoplasts and vacuoles. Nature 187:927–929

67. Takebe I, Labib C, Melchers G (1971) Regeneration of whole plants from isolated mesophyll protoplasts of tobacco. Naturwissenschaften 58:318–320 68. Carlson PS, Smith HH, Dearing RD (1972) Parasexual interspecific plant hybridization. Proc Natl Acad Sci USA 69:2292–2294 69. Braun AC (1941) Development of secondary tumor and tumor strands in the crown-gall of sunflowers. Phytopathology 31:135–149 70. Braun AC, White PR (1943) Bacteriological sterility of tissues derived from secondary crown-gall tumors. Phytopathology 33: 85–100 71. Braun AC (1950) Thermal inactivation studies on the tumor inducing principle in crowngall. Phytopathology 40:3 72. Zaenen I, van Larebeke N, Touchy H et al (1974) Super-coiled circular DNA in crowngall inducing Agrobacterium strains. J Mol Biol 86:109–127 73. Ledoux L (1965) Uptake of DNA by living cells. Prog Nucleic Acid Res Mol Biol 4:231–267 74. Vasil IK (ed) (1994) Cell culture and somatic cell genetics of plants, vol 1, Laboratory procedures and their applications. Academic, New York 75. Vasil IK, Thorpe TA (eds) (1994) Plant cell and tissue culture. Kluwer, Dordrecht 76. Yeoman MM, Street HE (1977) General cytology of cultured cells. In: Street HE (ed) Plant tissue and cell culture. Blackwell, Oxford, pp 137–176 77. Lindsey K, Yeoman MM (1985) Dynamics of plant cell cultures. In: Vasil IK (ed) Cell culture and somatic cell genetics of plants, vol 2. Academic, New York, pp 61–101 78. Fowke LC (1986) Ultrastructural cytology of cultured plant tissues, cells, and protoplasts. In: Vasil IK (ed) Cell culture and somatic cell genetics of plants, vol 3. Academic, New York, pp 323–342 79. Fowke LC (1987) Investigations of cell structure using cultured cells and protoplasts. In: Green CE, Somers DA, Hackett WP, Biesboer DD (eds) Plant tissue and cell culture. A. R. Liss, New York, pp 17–31 80. D’Amato F (1978) Chromosome number variation in cultured cells and regenerated plants. In: Thorpe TA (ed) Frontiers of plant tissue culture 1978. Intl. Assoc. Plant Tissue Culture, Univ. of Calgary Printing Services, Calgary, pp 287–295 81. Nagl W, Pohl J, Radler A (1985) The DNA endoreduplication cycles. In: Bryant JA, Francis D (eds) The cell division cycle in plants.

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120. Jacobs M, Negrutiu I, Dirks R, Cammaerts D (1987) Selection programmes for isolation and analysis of mutants in plant cell cultures. In: Green CE, Somers DA, Hackett WP et al (eds) Plant tissue and cell culture. A. R. Liss, New York, pp 243–264 121. Hughes K (1983) Selection for herbicide resistance. In: Evans DA, Sharp WR, Ammirato PV et al (eds) Handbook of plant cell culture, vol 1. MacMillan, New York, pp 442–460 122. Ranch JP, Rick S, Brotherton JE, Widholm J (1983) Expression of 5-methyltryptophan resistance in plants regenerated from resistant cell lines of Datura innoxia. Plant Physiol 71:136–140 123. Binding H (1986) Regeneration from protoplasts. In: Vasil IK (ed) Cell culture and somatic cell genetics of plants, vol 3. Academic, New York, pp 259–274 124. Evans DA, Sharp WR, Bravo JE (1984) Cell culture methods for crop improvement. In: Evans DA, Sharp WR, Ammirato PV et al (eds) Handbook of plant cell culture, vol 2. MacMillan, New York, pp 47–68 125. Schieder O, Kohn H (1986) Protoplast fusion and generation of somatic hybrids. In: Vasil IK (ed) Cell culture and somatic cell genetics of plants, vol 3. Academic, New York, pp 569–588 126. Chetrit P, Mathieu C, Vedel F et al (1985) Mitochondrial DNA polymorphism induced by protoplast fusion in Cruciferae. Theor Appl Genet 69:361–366 127. Potrykus I, Shillito RD, Saul M et al (1985) Direct gene transfer: state of the art and future potential. Plant Mol Biol Rep 3:117–128 128. Deshayes A, Herrera-Estrella L, Caboche M (1985) Liposome-mediated transformation of tobacco mesophyll protoplasts by an Escherichia coli plasmid. EMBO J 4:2731–2739 129. Crossway A, Oakes JV, Irvine JM et al (1986) Integration of foreign DNA following microinjection of tobacco mesophyll protoplasts. Mol Gen Genet 202:179–185 130. Klein TM, Wolf BD, Wu R et al (1987) Highvelocity microprojectiles for delivering nucleic acids into living cells. Nature 327:70–73 131. DeBlock M, Herrera-Estrella L, van Montague M et al (1984) Expression of foreign genes in regenerated plants and in their progeny. EMBO J 3:1681–1689 132. Borsch RB, Fraley RT, Rogers SG et al (1984) Inheritance of functional foreign genes in plants. Science 223:496–498 133. Gasser CS, Fraley RT (1989) Genetically engineering plants for crop improvement. Science 244:1293–1299

2 134. Uchimiya H, Handa T, Brar DS (1989) Transgenic plants. J Biotechnol 12:1–20 135. Kartha KK (1981) Meristem culture and cryopreservation methods and applications. In: Thorpe TA (ed) Plant tissue culture: methods and applications in agriculture. Academic, New York, pp 181–211 136. Dodds J (1989) Tissue culture for germplasm management and distribution. In: Cohen JI (ed) Strengthening collaboration in biotechnology: international agricultural research and the private sector. Bureau of Science and Technology, AID, Washington, DC, pp 109–128 137. Withers LA (1985) Cryopreservation of cultured cells and meristems. In: Vasil IK (ed) Cell culture and somatic cell genetics of plants, vol 2. Academic, New York, pp 253–316 138. Murashige T (1978) The impact of plant tissue culture on agriculture. In: Thorpe TA (ed) Frontiers of plant tissue culture 1978. Intl. Assoc. Plant Tissue Culture, Univ. of Calgary Printing Services, Calgary, pp 15–26 139. Conger BV (ed) (1981) Cloning agricultural plants via in vitro techniques. CRC, Boca Raton 140. Murashige T (1990) Plant propagation by tissue culture: practice with unrealized potential. In: Evans DA, Sharp WR, Ammirato PV, Bajaj YPS (eds) Handbook of plant cell culture, vol 5. McGraw-Hill, New York, pp 3–9 141. Zimmerman RH (1986) Regeneration in woody ornamentals and fruit trees. In: Vasil IK (ed) Cell culture and somatic cell genetics of plants, vol 3. Academic, New York, pp 243–258 142. Zenk MH (1978) The impact of plant cell culture on industry. In: Thorpe TA (ed) Frontiers of plant tissue culture 1978. Intl. Assoc. Plant Tissue Culture, Univ. of Calgary Printing Services, Calgary, pp 1–13 143. Wink M (1987) Physiology of the accumulation of secondary metabolites with special reference to alkaloids. In: Constabel F, Vasil IK (eds) Cell culture and somatic cell genetics of plants, vol 4. Academic, New York, pp 17–42 144. Dougall DK (1987) Primary metabolism and its regulation. In: Green CE, Somers DA, Hackett WP, Biesboer DD (eds) Plant tissue and cell culture. A. R. Liss, New York, pp 97–117 145. Kemp HA, Morgan MRA (1987) Use of immunoassays in the detection of plant cell products. In: Constabel F, Vasil IK (eds) Cell culture and somatic cell genetics of plants, vol 4. Academic, New York, pp 287–302 146. Widholm JM (1987) Selection of mutants which accumulate desirable secondary prod-

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159. Palmer CE, Keller WA (1994) In vitro culture of oil-seeds. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 413–455 160. Zimmerman RH, Swartz HJ (1994) In vitro culture of temperate fruits. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 457–474 161. Grosser IW (1994) In vitro culture of tropical fruits. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 475–496 162. Krikorian AD (1994) In vitro culture of plantation crops. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 497–537 163. Harry IS, Thorpe TA (1994) In vitro culture of forest trees. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 539–560 164. Debergh P (1994) In vitro culture of ornamentals. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 561–573 165. Karp A (1994) Origins, causes and uses of variation in plant tissue cultures. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 139–151 166. Dix PE (1994) Isolation and characterisation of mutant cell lines. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 119–138 167. Feher A, Dudits D (1994) Plant protoplasts for cell fusion and direct DNA uptake: culture and regeneration systems. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 71–118 168. Kartha KK, Engelmann F (1994) Cryopreservation and germplasm storage. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 195–230 169. Redenbaugh K (ed) (1993) Synseeds: applications of synthetic seeds to crop improvement. CRC, Boca Raton 170. Lowe KC, Davey MR, Power JB (1996) Plant tissue culture: past, present and future. Plant Tissue Cult Biotechnol 2:175–186 171. Kong L, Attree SM, Evans DE et al (1998) Somatic embryogenesis in white spruce: studies of embryo development, cell biology. In: Jain SM, Gupta PK (eds) Somatic embryogenesis in woody plants, vol 4. Kluwer, Dordrecht, pp 1–28 172. Kaeppler SM, Phillips RL (1993) DNA methylation and tissue culture-induced variation in plants. In Vitro Cell Dev Biol 29P: 125–130

173. Komamine A, Ito M, Kawahara R (1993) Cell culture systems as useful tools for investigation of developmental biology in higher plants: analysis of mechanisms of the cell cycle and differentiation using plant cell cultures. In: Soh WY, Liu JR, Komamine A (eds) Advances in developmental biology and biotechnology of higher plants, Proceedings first Asia Pacific Conference on plant cell and tissue culture, Taedok Science Town, Taejon, Korea, 5–9 Sept 1993, The Korean Society of Plant Tissue Culture, pp 289–310 174. Trehin C, Planchais S, Glab N et al (1998) Cell cycle regulation by plant growth regulators: involvement of auxin and cytokinin in the re-entry of Petunia protoplasts into the cell cycle. Planta 206:215–224 175. Gaspar T (1995) The concept of cancer in in vitro plant cultures and the implication of habituation to hormones and hyperhydricity. Plant Tissue Cult Biotechnol 1:126–136 176. Suguira M (1997) In vitro transcription systems from suspension-cultured cells. Annu Rev Plant Physiol Plant Mol Biol 48:383–398 177. Stitt M, Sonnewald U (1995) Regulation of carbohydrate metabolism in transgenics. Annu Rev Plant Physiol Plant Mol Biol 46:341–368 178. Kutchin TM (1998) Molecular genetics of plant alkaloid biosynthesis. In: Cordell G (ed) The alkaloids, vol 50. Academic, San Diego, pp 257–316 179. Verpoorte R, van der Heijden R, ten Hoopen HJG et al (1998) Metabolic engineering for the improvement of plant secondary metabolite production. Plant Tissue Cult Biotechnol 4:3–20 180. The Plant Cell, Special Issue, July 1997: Plant vegetative development: from seed and embryo to shoot and root. Larkins B (ed) 181. Fukuda H (1997) Xylogenesis: initiation, progression, and cell death. Annu Rev Plant Physiol Plant Mol Biol 47:299–325 182. Thorpe TA (1993) Physiology and biochemistry of shoot bud formation in vitro. In: Soh WY, Liu JR, Komamine A (eds) Advances in developmental biology and biotechnology of higher plants, Proceedings first Asia Pacific conference on plant cell and tissue culture, Taedok Science Town, Taejon, Korea, 5–9 Sept 1993, The Korean Society of Plant Tissue Culture, pp 210–224 183. Joy IVRW, Thorpe TA (1999) Shoot morphogenesis: structure, physiology, biochemistry and molecular biology. In: Soh WY, Bhojwani SS (eds) Morphogenesis in plant tissue cultures. Kluwer, Dordrecht, pp 171–214

2 184. Nomura K, Komamine A (1995) Physiological and biochemical aspects of somatic embryogenesis. In: Thorpe TA (ed) In vitro embryogenesis in plants. Kluwer, Dordrecht, pp 249–265 185. Dudits D, Györgyey J, Bögre L et al (1995) Molecular biology of somatic embryogenesis. In: Thorpe TA (ed) In vitro embryogenesis in plants. Kluwer, Dordrecht, pp 267–308 186. Thorpe TA, Stasolla C (2001) Somatic embryogenesis. In: Bhojwani SS, Soh WY (eds) Current trends in the embryology of angiosperms. Kluwer, Dordrecht, pp 279–336 187. Hinchee MAW, Corbin DR, Armstrong CL et al (1994) Plant transformation. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 231–270 188. Fraley RT, Rogers SG, Borsch RB et al (1985) The SEV system: a new disarmed Ti plasmid vector system for plant transformation. Bio/ Technology 3:629–635 189. Horsch RB, Fry J, Hoffman N et al (1985) A simple and general method for transferring genes into plants. Science 227:1229–1231 190. Cloutier S, Landry B (1994) Molecular markers applied to plant tissue culture. In Vitro Cell Dev Biol 31P:32–39

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191. Sanford JC (2000) The development of the biolistic process. In Vitro Cell Dev Biol 36:303–308 192. Fraley R (1992) Sustaining the food supply. Bio/Technology 10:40–43 193. Potrykus I (2001) The Golden Rice tale. In Vitro Cell Dev Biol Plant 37:93–100 194. Altman A, Ziv M, Izhar S (eds) (1999) Plant biotechnology and in vitro biology in the 21st century. In: Proceedings of the IXth international congress of the International Association for Plant Tissue Culture and Biotechnology, Jerusalem, 14–19 June 1998. Kluwer, Dordrecht 195. Vasil IK (ed) (2003) Plant biotechnology 2002 and beyond. In: Proceedings of the 10th IAPTC&B Congress, 23–28 June 2002, Orlando, FL. Kluwer, Dordrecht 196. Xu Z, Li J, Xue Y, Yang W (eds) (2007) Biotechnology and sustainable agriculture 2006 and beyond. In: Proceedings of the 11th IAPTC&B Congress, 13–18 Aug 2006, Beijing. Springer, Dordrecht 197. Schell J (1995) Progress in plant sciences is our best hope to achieve an economically rewarding, sustainable and environmentally stable agriculture. Plant Tissue Cult Biotechnol 1:10–12

Chapter 3 Callus, Suspension Culture, and Hairy Roots. Induction, Maintenance and Characterization Rosa M. Galáz-Ávalos, Sagrario Aguilar-Díaz, Pedro A. Xool-González, Silvia M. Huchín-May, and Víctor M. Loyola-Vargas Abstract The growth is a characteristic of each culture and it is determinate by the origin of the species, culture conditions, and type of culture. In this chapter, we make a comparison of the different growth parameters among three different species and three different types of cultures. Key words: Callus, Conductivity, Growth, Hairy roots, Suspension cultures

1. Introduction Callus induction is necessary, as the first step, in many tissue culture experiments. Callus is produced when the initial response of the tissues to a wound is followed by the external addition of growth regulators in an aseptic medium in order to maintain the rapid cell division response and sustain it indefinitely (1). Callus formation from an explant involves the development of progressively more random planes of cell division, less frequent specialization of cells, and loss of organized structures (2, 3). Calli can be obtained from almost any part of the plant. However, it must be taken into account that different factors can influence the initiation of the calli. These factors include the physiological or ontogenic age of the organ or tissue that serves as the explant source; the environmental conditions in which the plant is cultivated before the explant is taken; the organization of the cells; and the size and location of the explant in the plant. Another consideration to keep in mind is the ultimate goal of the cell culture (4), and the fact that not all the cells in the explant produce callus.

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_3, © Springer Science+Business Media, LLC 2012

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The source of the primary explant can be an aseptically germinated seedling or surface-sterilized roots, stems, leaves, or reproductive structures. The level and kind of plant growth regulators as well as the culture medium are the major factors that control callus formation. Culture conditions are also important in callus formation and development as well as the level of gases inside the flask or container. For the subculture of callus, small portions of friable callus, normally 0.2–0.5 g, must be transferred to the new medium in order to have fresh callus. The calli can be used as a source of material for biochemical and molecular studies, and to produce suspension cultures, protoplasts, organogenesis, somatic embryos, and secondary metabolites (1, 4). Calli cultures are normally maintained in growth chambers under controlled light conditions, which need to be established for each species and genotypes. Also, for most species, the callus cultures need to be maintained at a temperature of 25°C. Callus cultures are subcultured under these conditions every 2–6 weeks depending on the growth rate (5). Cell suspension culture consists of a population of single cells and clumps suspended from a single callus, in flasks with liquid nutrient medium (6). The flasks are then placed on a shaker with constant agitation to provide aeration to the cells (7–9). As new cells are formed, they are dispersed into the liquid medium and become clusters and aggregates (9). In general, cells in suspension exhibit much higher rates of growth than cells in callus culture. The suspension cultures are used when rapid cell division or a more uniform treatment application is required, such as during cell selection procedures. Cell suspension can be maintained by transferring a small portion of the culture into fresh medium. 1.1. Growth Curves

The callus and cell suspension cultures’ growth rate parallels in many ways to a sigmoid curve seen in populations of single-celled organisms (10). There are several stages of growth (10, 11) independently whether the culture is callus, cell suspension, or hairy root culture. A typical growth curve for fresh weight and dry weight of different cultures is shown in Figs. 1–4. There is an initial lag phase (I) followed by a period of rapid growth which may approach exponential (II), then lineal (III), a period of declining growth after the lineal phase begins (IV) followed by a stationary phase (V), and eventually a decline in the biomass as the cells in the culture begin to senesce. The behavior of the cells is different during each growth stage. There are several factors influencing the growth of the cells, such as the culture medium, origin of the explant, growth regulators’ amount, environmental culture conditions, etc. The cultures must be transferred to fresh medium before they reach the stationary phase. The deceleration of growth is due to several factors; among them are the depletion of nutrients, cell density, and production of toxic by-products.

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Fig. 1. Growth cycle for Jatropha curcas. Fresh weight (filled circle) and dry weight (filled square). A gram of callus is inoculated in 25 mL of MS medium supplemented with 2.69 μM naphthalene acetic acid and 4.64 μM kinetin contained in baby food jars. The flasks are incubated under dark conditions at 25 ± 2°C. Triplicate samples are taken every 4 days, beginning with day 0, until day 40.

The first two phases of growth of the culture are the exponential and linear. The culture must be transferred to fresh medium at the end of the linear phase (phase number III). Cells’ growth can be monitored measuring different parameters depending on the cultures, such as fresh and dry weight, cell number, medium conductivity, percentage of the cell packet, image analysis, light absorbance, osmolarity, focused beam reflectance, image processing, enzymatic activity, and turbidimetric measurement (12–21). The behavior of the tissue culture is different during each stage of growth. The medium and the incubation conditions can affect how long the callus remains at a particular stage (4). For many experimental procedures, it is necessary to use cultures at a specific developmental point. This is the reason why it is very important to characterize the growth cycle before to start with any experiment. During the whole growth cycle, the viability must be checked up in order to make sure that the culture is growing properly. The viability can be followed using different methods; among them, dye exclusion (22, 23), vital dying (24), and electron transport activity (25) are the most used. Viability can also be determined by noninvasive methods (26) or using intracellular esterase activity (27). In some cases, the reduction of tetrazolium salts can be a better indicator of metabolically active cells, such as in the study of reactive oxygen species-mediated responses during the critical early hours of fungal elicitation (28).

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Fig. 2. Growth of Coffea arabica suspension culture line L1. (a) Fresh weight (filled circle); dry weight (filled square); conductivity (filled inverted triangle). (b) Cell number (filled circle); cellular packet (filled square). One hundred milligrams of cells are transferred into 25 mL of MS medium supplemented with 13.6 μM 2,4-D and 4.4 μM BA contained in baby food jars. The flasks are incubated under photoperiod (16-h light to 8-h dark at 25 ± 2°C). Triplicate samples are taken every 2 days, beginning with day 0, until day 24.

2. Materials 2.1. Biological Material

2.1.1. Jatropha curcas L. plants in in vitro culture. 2.1.2. Coffea arabica L. plants in in vitro culture. 2.1.3. Catharanthus roseus plants in in vitro culture. 2.1.4. Agrobacterium rhizogenes.

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Fig. 3. Growth of Coffea arabica suspension culture line L2. (a) Fresh weight (filled circle); dry weight (filled square); conductivity (filled inverted triangle). (b) Cell number (filled circle); cellular packet (filled square). One hundred milligrams of cells are transferred into 25 mL of MS medium supplemented with 13.6 μM 2,4-D and 4.4 μM BA contained in baby food jars. The flasks are incubated under photoperiod (16-h light to 8-h dark at 25 ± 2°C). Triplicate samples are taken every 3 days, beginning with day 0, until day 42.

2.2. Glassware

1. Erlenmeyer flasks (250 mL). 2. Glass bottles (250 mL). 3. Petri dishes (100 × 15 mm). 4. Beakers (500–1,000 mL). 5. Baby food jars.

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Fig. 4. Growth of Catharanthus roseus hairy roots. Fresh weight (filled circle). Conductivity or (Co − Cf) (filled square). Half of a gram of the hairy roots is transferred into 50 mL of B5 half strength without growth regulators in 250-mL Erlenmeyer flasks. The flasks are incubated under dark conditions at 25 ± 2°C. Triplicate samples are taken every day.

2.3. Instrumentation

1. Analytical balance. 2. Hot/stirrer plate. 3. pH meter. 4. Autoclave. 5. Conductimeter. 6. Centrifuge. 7. Hemocytometer. 8. Laminar flow cabinet. 9. Bunsen burner. 10. Micropipets. 11. Microscope. 12. Sterile Petri dishes.

2.4. Chemicals

1. Plant growth regulators: 2,4-dichlorophenoxy acetic acid (2,4-D); naphthalene acetic acid (NAA); kinetin (K); benzyl adenine (BA). 2. Murashige and Skoog (MS) culture medium (29). 3. Gambor (B5) medium (7). 4. Commercial bleach solution (Cloralex®). 5. Tween 20. 6. Sterile distilled water.

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7. Agar. 8. Ethyl alcohol. 9. Trypane blue. 10. Fluorescein triacetate. 11. Chromium trioxide.

3. Methods 3.1. Induction 3.1.1. Establishment of Jatropha curcas Callus Cultures

Two-month-old J. curcas plantlets cultivated in vitro are used as a source for the explants. Leaves explants, eliminating midvein and edges, are put in baby food jars with 25 mL of solid (agar) MS medium with 2.69 μM NAA and 4.64 μM K under dark conditions at 25 ± 2°C. The calli appear around the wounding after 1 week. After 4 weeks, the calli obtained are separated from the original leave explant and transferred into a fresh medium. The callus cultures are first selected for their ability to accumulate biomass. Once established, the calli are subcultured every 30 days.

3.1.2. Establishment of Coffea arabica Callus and Suspension Cultures

Three-month-old C. arabica plantlets cultivated in vitro are used as a source for the explants. Leaves explants, eliminating midvein and edges, are put in baby food jars with 25 mL of solid MS medium (agar) supplemented with 13.52 μM 2,4-D and 4.43 μM BA under dark conditions at 25 ± 2°C. The calli appear around the wounding after 3 weeks and they are transferred into a fresh medium. The callus cultures are first selected for their ability to accumulate biomass. Once established, the calli are subcultured every 30 days. Two grams of C. arabica calli in the linear phase of growth are transferred to a 250-mL Erlenmeyer flask with 50 mL of MS medium supplemented with 13.52 μM 2,4-D and 4.43 μM BA. The callus is disaggregating with a sterilized forceps inside of a laminar flow cabinet. The flasks are incubated in a shaker at 100 rpm under dark conditions at 25 ± 2°C. After 4 weeks, the culture is filtered through a 60-μm mesh in order to eliminate the big pieces of callus. The cells and clumps are precipitated by centrifugation (1892 × g) and the old medium is eliminated and replaced with new medium. After two or three transferences, the growth of the cells is good enough to dilute and start the suspension culture. Five milliliters of the stock solution of C. arabica suspension culture are transferred into 45 mL of fresh MS medium supplemented with 4.5 μM 2,4-D and 9.2 μM BA in 250-mL Erlenmeyer flasks. The cultures are subcultured every 14 days.

3.1.3. Establishment of Transformed Root Cultures

The A. rhizogenes strain 1855 pBI 121.1 is cultured in solid yeast extract-mannitol broth (YMB) medium (pH 8) at 25°C for 2 weeks before it is transferred into 50-mL Erlenmeyer flasks containing

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10 mL of liquid yeast extract-tryptone (YT) medium. The flasks are incubated at 25°C in the dark in a gyratory shaker (100–120 rpm) for 48 h. An aliquot (1.5 mL) is taken and centrifuged for 3 min at 14,000 × g. The supernatant is eliminated and the pellet resuspended in 300 μL of YT medium to a final concentration of 1.7 × 105 bacteria per microliter. This suspension is used for the infection of explants. Two-month-old C. roseus plantlets are dissected in a sterile Petri dish. Leaves and stems are put in baby food jars with 25 mL of solid B5 medium (7) at half ionic strength for both major and minor components and vitamins, without growth regulators and supplemented with 1 mg/mL of antibiotic (carbenicillin or cephatoxime, depending on the A. rhizogenes strain used). The leaves must be placed in such a way that the upper surface touches the medium and the extreme end of the petiole remaines exposed. In the case of stems, the apical part is exposed. Four stems or two leaves must be placed in each jar. An aliquot of 5 μL of the bacteria solution is applied to the wounded area of each of the explants. For each bacterial strain, 40 leaves and 20 stem cuts are infected. The infected explants are incubated at 25 ± 2°C in the dark in a growth chamber. The roots obtained from the explants infected by the bacteria are harvested when they are approximately 1 cm long. The roots are placed in a solid B5 medium, at half ionic strength, with 1 mg/mL of antibiotic. After several transfers to eliminate the bacteria, the axenic root cultures are put in liquid B5 medium at half ionic strength. The root cultures are first selected for their ability to accumulate biomass and scaled up to 250-mL flasks with 100 mL of medium. Once established, the hairy roots are subcultured every 18–25 days (30). 3.2. Measurement of Growth 3.2.1. Jatropha curcas Calli

In order to characterize the growth of the J. curcas calli, a growth curve must be established. A gram of callus is inoculated in 25 mL of MS medium supplemented with 2.69 μM NAA and 4.64 μM kinetin contained in baby food jars. The flasks are incubated under dark conditions at 25 ± 2°C. Triplicate samples are taken every 4 days, beginning with day 0, until day 40. Every sample is weighted immediately in order to measure the fresh weight. This is a nondestructive method. After the samples are weighted, they are freezed with liquid nitrogen and stored at −80 C until the last sample is finished and freeze-dried. The freeze-dried samples are weighted in order to get the dry weight. Dry weight is a more reliable criterion to follow growth than fresh weight, but this method requires sacrifice of the samples. The results of fresh and dry weight are shown in Fig. 1a, b. After the growth cycle curve is built, the data are analyzed by using the doubling time software package (Roth V. 2006 http://www. doubling-time.com/compute.php) (Table 1).

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Table 1 Growth parameters of the tested cultures Species

Culture

Technique

Doubling time (days)

Growth rate

Growth index

Jatropha curcas

Calli

FWa DW

7.95 12.95

0.0871 0.0535

1.96 0.86

Coffea arabica L1

Suspension culture

FW DW NC C CP

3.62 3.69 2.95 3.35 4.82

0.1916 0.1877 0.2346 0.2068 0.1437

3.51 5.63 4.72 5.36 3.37

C. arabica L2

Suspension culture

FW DW NC C CP

3.55 4.86 4.84 4.76 4.86

0.1954 0.1425 0.1433 0.1456 0.1427

10.12 4.41 5.48 4.73 4.25

Catharanthus roseus

Hairy roots

FW C

3.53 3.14

0.2289 0.2207

3.04 2.37

a

Fresh weight (FW); dry weight (DW); number of cells (NC); conductivity (C)

3.2.2. Coffea arabica Suspension Culture

In order to characterize the growth of the C. arabica suspension culture, a growth curve must be established. One hundred milligrams of cells are transferred into 25 mL of MS medium supplemented with 13.6 μM 2,4-D and 4.4 μM BA contained in baby food jars. The flasks are incubated under photoperiod (16-h light to 8-h dark at 25 ± 2°C). Triplicate samples are taken every 2 days (L1), beginning with day 0, until day 24, or every 3 days (L2), beginning with day 0, until day 42. Growth of suspension cultures is measured by filtering the cell suspension through a wet Whatman No. 1 filter paper with a funnel attached to a vacuum line. The vacuum is maintained until the excess medium is removed as judged by the appearance of the cell mass. The cells are then carefully scraped off from the surface of the paper and transferred into a preweighed vial. The vials are kept at −80°C and freeze-dried later in order to get the dry weight. The results are shown in Figs. 2 and 3. Another method to measure the growth of the suspension cultures is counting the number of cells. In order to determine the number of cells (density) in each flask, an aliquot of the suspension culture is allocated into a hemocytometer and the cells are counted under a microscope. The results are reported as cells per milliliter (Figs. 2b and 3b). An additional method to measure the suspension culture growth is by the packet cell volume. Ten milliliters of the suspension culture are put in a conical graduate tube and centrifuged at 1892 ´g in a centrifuge for 15 min at room temperature. The packet formed by the cells is recorded, and the volume of the cells

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expressed as a percentage of the volume of cell suspension is used to follow the growth of the culture (Figs. 2b and 3b). 3.2.3. Catharanthus roseus Hairy Roots

In order to characterize the growth of the C. roseus hairy roots culture, a growth curve must be established. Half of a gram of the hairy roots is transferred into 50 mL of B5 half strength without growth regulators in 250-mL Erlenmeyer flasks. The flasks are incubated under dark conditions at 25 ± 2°C. Triplicate samples are taken every day. The medium is used to measure the conductivity and the roots are used for fresh and dry weight determination as already mentioned above (Fig. 4). After a growth cycle curve is built, the data are analyzed by using the following formula. To calculate the speed of growth, the following formula can be used: μ=

ln X f − ln X 0 , tf − t0

where μ = growth speed; Xf = final weight; X0 = initial weight; tf = final time; and t0 = initial time. In order to calculate the duplication time of the culture, the following formula can be used: Td =

ln 2 , μ

where Td = duplication time and μ = the speed of growth. To calculate the growth index, the following formula can be used: I =

Xf − X0 , X0

where I is the growth index, Xf is the final weight, and X0 is the initial weight. The growth of the three species described in this chapter shows a similar growth curve with an initial lag phase, an exponential phase, and a stationary phase (Figs. 1–4). The major difference is that the growth cycle is completed more rapidly in suspension and hairy root cultures than in callus cultures (Table 1). The duplication time of C. roseus hairy roots is 3.53 days using the fresh weight as a parameter to follow the growth of the roots. When the conductivity is used instead of the fresh weight, the duplication time is 3.14 days. Similar results were found for the other three cultures. For the C. arabica L1, the duplication time oscillated between 2.95 and 4.82 days when we used the number of cells and the cellular packet to calculate its growth, respectively. However, the calculation of the duplication time using fresh and dry weight as well as cell number gives a very close result around 3.6 days.

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Acknowledgment This work was supported by a grant from CONACYT for Jatropha work. References 1. Hall RD (1991) The initiation and maintenance of callus cultures of carrot and tobacco. In: Lindsey K (ed) Plant tissue culture manual. Supplement 3. Kluwer, The Netherlands, pp 1–19 2. Thorpe TA (1980) Organogenesis in vitro: structural, physiological and biochemical aspects. Int Rev Cytol Suppl 11A:71–111 3. Wagley LM, Gladfelter HJ, PHILLIPS GC (1987) De novo shoot organogenesis of Pinus eldarica Medw. in vitro. II. Macro- and microphotographic evidence of de novo regeneration. Plant Cell Rep 6:167–171 4. Smith RH (1992) Plant tissue culture. Techniques and experiments. Academic, San Diego 5. Collin HA, Edwards S (1998) Plant cell culture. Springer, New York, NY 6. Hall RD (1991) The initiation and maintenance of plant cell suspension cultures. In: Lindsey K (ed) Plant tissue culture manual. Supplement 3. Kluwer, The Netherlands, pp 1–21 7. Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50:151–158 8. Street HE (1977) Cell suspension cultures. Techniques. In: Street HE (ed) Plant tissue and cell culture. University of California Press, Oxford, pp 61–102 9. Morris P, Fowler MW (1981) A new method for the production of fine plant cell suspension cultures. Plant Cell Tiss Org Cult 1:15–24 10. Davis BD, Dulbecco R, Eisen HN et al (1978) Tratado de Microbiología. Con Inclusión de Inmunología y Genética Molecular. Salvat Editores, S.A., Barcelona 11. Phillips GC, Hubstenberger JF, Hansen EE (1995) Plant regeneration by organogenesis from callus and cell suspension cultures. In: Gamborg OL, Phillips GC (eds) Plant cell, tissue and organ culture. Fundamental methods. Springer-Verlag, Germany, pp 67–79 12. Coles GD, Abernethy DJ, Christey MC et al (1991) Monitoring hairy-root growth by image analysis. Plant Mol Biol Rep 9:13–20

13. Hahlbrock K, Kuhlen E (1972) Relationship between growth of parsley and soybean cells in suspension cultures and changes in the conductivity of the culture medium. Planta 108:271–278 14. James E, Lee JM (2000) An improved optical technique for monitoring plant cell concentration. Plant Cell Rep 19:283–285 15. Madhusudhan R, Rao SR, Ravishankar GA (1995) Osmolarity as a measure of growth of plant cells in suspension cultures. Enzyme Microb Technol 17:989–991 16. Mills DR, Lee JM (1996) A simple, accurate method for determining wet and dry weight concentrations of plant cell suspension cultures using microcentrifuge tubes. Plant Cell Rep 15:634–636 17. Nicoloso FT, Val J, Van der Keur M et al (1994) Flow-cytometric cell counting and DNA estimation for the study of plant cell population dynamics. Plant Cell Tiss Org Cult 39: 251–259 18. Olofsdotter M (1993) Image processing: a non-destructive method for measuring growth in cell and tissue culture. Plant Cell Rep 12: 216–219 19. Shetty K, Bothra D, Crawford DL et al (1990) Extracellular peroxidases as indicators of growth in plant cell suspension cultures. Appl Biochem Biotechnol 24(25):213–221 20. Sung ZR (1976) Turbidimetric measurement of plant cell culture growth. Plant Physiol 57:460–462 21. Vitecek J, Adam V, Petek J et al (2004) Esterases as a marker for growth of BY-2 tobacco cells and early somatic embryos of the Norway spruce. Plant Cell Tiss Org Cult 79:195–201 22. Huang C-N, Cornejo MJ, Bush DS et al (1986) Estimating viability of plant protoplasts using double and single staining. Protoplasma 135:80–87 23. Baker CJ, Mock NM (1994) An improved method for monitoring cell death in cell suspension and leaf disc assays using Evans blue. Plant Cell Tiss Org Cult 39:7–12

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24. Widholm JM (1982) The use of fluorescein diacetate and phenosafranine for determining viability of cultured plant cells. Stain Technol 47:189–194 25. Suzuki T, Yoshioka T, Kato Y et al (1987) A new estimation method for plant cell viability by determining electron transport activity. Plant Cell Rep 6:279–282 26. Sowa S, Towill LE (1991) Infrared spectroscopy of plant cell cultures. Noninvasive measurement of viability. Plant Physiol 95:610–615 27. Steward N, Martin R, Engasser JM et al (1999) A new methodology for plant cell viability assessment using intracellular esterase activity. Plant Cell Rep 19:171–176

28. Escobedo-GraciaMedrano RM, MirandaHam ML (2003) Analysis of elicitor induced cell viability changes in Lycopersicon esculentum Mill suspension culture by different methods. In Vitro Cell Dev Biol-Plant 39: 236–239 29. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15: 473–497 30. Ciau-Uitz R, Miranda-Ham ML, CoelloCoello J et al (1994) Indole alkaloid production by transformed and non-transformed root cultures of Catharanthus roseus. In Vitro Cell Dev Biol-Plant 30:84–88

Chapter 4 Growth Measurements: Estimation of Cell Division and Cell Expansion Gregorio Godoy-Hernández and Felipe A. Vázquez-Flota Abstract The main parameters for the estimation of growth within in vitro cultures are reviewed. Procedures to measure these parameters are described, emphasizing in each case their convenience of use, depending on the features of the culture evaluated. Key words: Cell counting, Duplication time, Dry weight, Fresh weight, Growth index, Packed cell volume

1. Introduction The accurate, fast, and reliable determination of cell growth is of critical importance in plant cell and tissue culture. The precise assessment of growth kinetics is essential for the efficient design of bioprocess engineering. However, the measurement of growth parameters in the different types of cultures and concomitantly the use of various containers along with the heterogeneity in cell morphology introduce diverse problems that must be addressed by using a specific methodology for each case (1). Since callus and cell suspension cultures represent two of the most common in vitro systems, this chapter concentrates on growth measurements in such systems. 1.1. Callus Cultures

Plant cell cultures are initiated through the formation of a mass of nondifferentiated cells called “callus.” A callus culture is obtained by excising a piece of tissue, the explant, from the parent plant and placing it onto a nutrient base, solidified with agar. This nutrient base contains macronutrients (nitrogen, potassium, phosphorus,

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_4, © Springer Science+Business Media, LLC 2012

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etc.), micronutrients (cobalt, copper, iron, etc.), a carbon source (usually sucrose), and various plant growth regulators. Callus tissue is not an ideal system to work with, due to their slow growth rate and high biochemical variability. Nevertheless, since they are an almost obligatory step to initiate an in vitro culture, the proper assessment of the effect of different media composition or growth regulators on their growth rate is an important parameter to define the optimal media to use. The most common growth parameters used for callus cultures include fresh weight, dry weight, and growth index. 1.2. Suspension Cultures

The success in the establishment of a cell suspension culture depends, in a great extent, on the availability of “friable” callus tissue, i.e., a tissue that, when stirred in liquid medium, rapidly disaggregates into single cells and small clusters. Such a system is much more amenable for biochemical studies and process development than calli, since they generally grow in a faster rate and allow cells to be in direct contact with the medium nutrients. Suspension or liquid cultures of plant cells are usually grown as microbial cells. However, plant cell dimensions are larger than those of bacteria or fungi, ranging from 20 to 40 μm in diameter and from 100 to 200 μm in length (2, 3). The central vacuole occupies a large portion of the mature cell volume. Plant cell cultures tend to contain clumps, formed by a variable number of cells. These clumps arise as a result of the failure of new cells to separate after division or from the adherence of free cells among themselves. In some cases, such clumps (also known as aggregates) may contain up to 200 cells, and reach up to 2 mm in diameter. Although cell stickiness can be overcome by modifying the culture medium, cells in culture become “sticky” in late lag phase of growth as a rule. Methods to obtain suspensions composed largely of free cells (fine cell suspensions) include the use of cell wall degrading enzymes and sieving. Unfortunately, once established, a fine cell suspension has a tendency with time to revert to a clumped condition (4).

1.3. Methods for Evaluating Growth in In Vitro Cultures

There are several methods for evaluating growth kinetics in plant cell cultures. Selected examples include: fresh cell weight, dry cell weight, settled cell volume, packed cell volume, cell counting, culture optical density, residual electrical conductivity, and pH measurements, among others (1). In cultures originated from different plant species, settled volume, packed cell volume, as well as fresh weight, all show a very good linear correlation with dry weight data. Thus, any of these estimations can be used for measuring cell growth. However, during the stationary phase of the culture, there are important deviations in this correlation. At this phase, plant cell cultures show a high degree of aggregation, cell lysis, and a marked heterogenity in cell morphology.

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The measurement of cell concentration by cell counting and turbidity (optical density) has also shown a reasonably good correlation with the dry cell weight parameter. When cultures reached the stationary phase, the same problems stated above render unsatisfactory results regarding to the correlation of these parameters to dry weight estimation. On the other hand, protein, RNA and DNA contents fail to show the same good correlation with the dry weight, which may be ascribed to changes in cell physiology along the growth cycle, which frequently results in wide variations. Although complicated and time consuming, cell counting represent the best way to assess culture growth in suspension cultures. Nevertheless, it often shows a good correlation with other parameters, such as electric conductivity. Cell density is obtained by direct counting of cells under the microscope, using a cell counting chamber, such as the Sedgewick rafter cell (Graticulates Limited, Tonbridge England) or the Newbauer chamber (Sigma-Aldrich, San Luis, MO). Such devices hold a fixed volume of the suspension over a defined area. The base of the chamber is divided in squares, frequently containing a 1 mm3 (1 μL) volume. By observing the suspension with a low magnification objective, cells contained in such a volume are identified and counted. The use of digital methods, consisting in the capture of a microphotography and then processing it with one the several software packages, such as MATLAB, MathWorks Co. (5), may significantly reduce the time invested in this kind of analysis. Recently, Millipore has developed a hand-held cell counter, based on the Coulter principle, or flow cytometry (the Scepter™), which might provide a fast and accurate cell estimation at an affordable cost. However, it has been designed for animal cells, which are smaller than plant cells (10–30 vs. 30–100 μm in diameter, respectively). Therefore, its application for plant cell cultures will be limited until this size restriction is overcome. Electric conductivity of culture medium decreases inversely to biomass gain. This is a consequence of ion uptake by cells. The monitoring of this decrease to assess cell growth offers several advantages over other methods, such as the following: (1) it allows continuous and in situ or on-line monitoring of cell growth; (2) no sampling or no wet chemical analysis is required; (3) it is economical and efficient; (4) it provides an accurate, reliable, and reproducible measurement of plant cell growth rate; and (5) it is independent of cell aggregation, growth morphology, and apparent viscosity (1).

2. Materials 2.1. Biological Material

1. Callus and cell suspension cultures of any species.

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2.2. Glassware

1. Glass desiccators, or any other hermetic container, with silica gel. 2. 50-mL sterile, graduated centrifuge tubes. 3. Counting cell chamber (Sedgewick rafter cell).

2.3. Instrumentation

1. Analytical balance (resolution to 0.01 mg). 2. Top loading balance (resolution 0.1 g). 3. Convection oven (resolution 0.1°C). 4. Conductivity meter (range 0–200 μS and 0–200 mS; resolution 0.1 units). 5. Universal centrifuge (with a speed range including 4,000 × g). 6. Light microscope with 10× and 40× objective lenses.

2.4. Chemicals

1. 8% chromium trioxide solution: Dissolve 8 g of CrO3 in 100 mL of water. Keep in the dark at room temperature. 2. 10% cellulase solution: Dissolve 0.5 g of cellulase from Aspergillus sp. (Sigma Chemical Co, St. Louis, MO) in 5 mL 100 mM KH2PO4, pH 6.0. Keep at 4°C. Use solution within a week. 3. 5% macerozyme R-10 solution: dissolve 0.25 g of Macerozyme R-10 (Pectinase from Rhizopus) (Sigma Chemical Co, St. Louis, MO), in 5 mL 100 mM KH2PO4, pH 6.0. Keep at 4°C. Use solution within a week.

3. Methods 3.1. Measuring Growth in Callus Cultures 3.1.1. Fresh-Weight Determination 3.1.2. Dry-Weight Determination

1. To determine the total fresh weight, harvest all the tissue on the media surface with flat-end tweezers and weigh on a balance. To avoid tissue desiccation, open the culture jar only when you are ready to processes it. 1. Dry weight can be estimated by drying the tissue at 60°C in a convection oven, until constant weight (usually 16 h). Take a sample of the fresh tissue, weigh it on a preweighed square of aluminum foil, and evaporate the water contained in the tissue in the preheated oven at 60°C for 12 h. 2. Allow samples to cool down in a desiccator containing silica gel for 15–20 min and then register the sample’s weight. 3. Put the tissue sample back into the oven and take a new weight register after 2 h. If no variations are detected, samples have reached constant weight. If variations higher than 10% regarding the previous register are observed, return samples to the oven for another 2 h period.

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4. Alternatively, dry weight can be obtained from lyophilized tissues. Once harvested, fresh tissues should be weighed, deposited in lyophilizer flasks and freezed at −20°C for at least 12 h. Flasks with frozen tissues are then connected to the vacuum line for 24 h and weight is registered. 3.2. Measuring Growth in Cells Cultures

Growth of suspension cultures is commonly evaluated as the settled cell volume (SCV), the packed cell volume (PCV), fresh cell weight (FCW), dry cell weight (DCW). Indirect evaluations include pH measurements and medium residual conductivity (mmhos). Finally, parameters describing growth efficiency, such as specific growth rate (m), doubling time (dt), and growth index, can be determined.

3.2.1. Settled Cell Volume and Packed Cell Volume

Both parameters allow for the quick estimation of culture growth while maintaining sterile conditions. These measurements are useful for monitoring growth in the same flasks along a culture cycle, since suspensions may be returned to prior culture conditions. Care must be taken to maintain sterile conditions. However, volume estimation may not be an accurate way of monitoring growth, given its dependence on cell morphology (cell and clump size, cell density, etc.). SCV is determined by allowing a cell suspension to sediment in graduated tubes. It is reported as the percentage of the total volume of suspension occupied by the cell mass. The PCV is determined in a similar way, after it has been compacted by centrifugation (see Note 1).

Settled Cell Volume

1. Pour the cell suspension in a graduated cylinder of adequate volume. 2. Allow the suspension to settle for 30 min and record the cell volume. 3. Take a second read 30 min later. If the variation between readings is higher than 5%, record a third measurement after another 30 min wait period. 4. The volume fraction of the suspension occupied by the cells is determined as the SCV.

Packed Cell Volume

3.2.2. Fresh Cell Weight and Dry Cell Weight

1. PCV can be determinated by centrifuging 10 mL of the culture in a 15-mL graduated conical centrifuge tube at 200 × g for 5 min. Fresh and dry cell weight represent more precise measurements of cell growth than the sole culture volume. However, both require the manipulation of samples in nonsterile conditions. Fresh weight estimation involves less time than that required for dry weight, but it may not reflect a real measurement of biomass gain, particularly

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at the end of the culture period, when most of the culture growth is due to water uptake (6). 1. Collect the cell mass by filtration, using a Büchner funnel under vacuum. 2. Wash the cell package with about 3 mL distilled water and retain under vacuum for a fixed time periods (e.g. 30 s). Weigh immediately to reduce variations due to water evaporation. 3. Fresh and dry weights are determined as described earlier for callus tissue. 3.2.3. Culture Cell Density

In order to obtain a reliable value of the number of cells in a suspension culture, clusters should be first disaggregated. This can be accomplished by incubating the suspension with an 8% chromium trioxide solution, or with hydrolytic enzymes, such as cellulase and pectinase. The chromium trioxide method is quicker and less complicated than the use of enzymes; however, it hinders the estimation of cell viability in the same sample. Since a careful use of enzymes maintains cells viable, the assessment of the number of living cells by the exclusion of vital stains can be performed in the same sample.

Cell Cluster Disaggregation by Chromium Trioxide

1. Take 1 mL of the cell suspension and add 2 mL of 8% CrO3. 2. Incubate the mixture for 15 min at 70°C. 3. Vortex the mixture vigorously for 15 min.

Cell Cluster Disaggregation Hydrolytic Enzymes

1. Take 1 mL of the cell suspension and mix it with 0.5 mL of 10% cellulase and 0.5 mL 5% pectinase. 2. Incubate 30 min at 25°C with rotatory agitation (100 rpm) (see Note 2).

Cell Counting

1. Fill the counting cell chamber with the mixture, position carefully the cover glass on top of the chamber, to avoid the formation of bubbles. 2. Observe under the microscope with the 10× objective to locate the squared field. 3. Count all the cells contained in ten squares. Add the values of the ten squares (do not obtain the average). This number represents the number of cells in 10 μL, so multiply by 100 to determine the cell number per mL (7) (see Note 3). 4. Depending on the culture’s cell density, further dilution may be required, which should be considered in the calculation.

3.3. Parameters of Growth Efficiency 3.3.1. Growth Index

Both, fresh and dry weight, are measurements of tissue’s absolute biomass at a given sampling time. No reference to the actual growth capacity is taken in consideration. Growth index is a relative

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estimation of such capacity as it correlates the biomass data at the sampling time to that of the initial condition. It is calculated as the ratio of the accumulated and the initial biomass. The accumulated biomass corresponds to the difference between the final and the initial masses. GI =

W F − W0 W0

where GI represents growth index, and WF and W0, represent the final and initial masses, respectively (either as fresh or dry weight). 3.3.2. Specific Growth Rate

It is generally accepted that growth of a cell culture with respect to time is best described by the sigmoid curve theory. At the beginning, the cell population grows relatively slow (lag phase). As the population size approaches one half of the carrying capacity (defined by the nutrient status of the culture medium), the culture’s growth per time unit increases. The rate of growth is measured by the steepness of the curve, and it is the steepest when the population density reaches one-half of the carrying capacity (in the middle of the sigmoid). After this point, the steepness of the curve decreases, keeping this tendency as the population increases, until it reaches the carrying capacity (stationary phase). The specific growth rate (m) refers to the steepness of such a curve, and it is defined as the rate of increase of biomass of a cell population per unit of biomass concentration. It can be calculated in batch cultures, since during a defined period of time, the rate of increase in biomass per unit of biomass concentration is constant and measurable. This period of time occurs between the lag and stationary phases. During this period, the increase in the cell population fits a straight line equation (7): ln x = mt + ln x 0 m=

ln x − ln x 0 t

where x0 is the initial biomass (or cell density), x is the biomass (or cell density) after time t, and m is the specific growth rate. 3.3.3. Doubling Time

Doubling time (dt) is the time required for the concentration of biomass of a population of cells to double. One of the greatest contrasts between the growth of cultured plant cells and microorganisms refers to their respective growth rates. While the pattern of growth may be the same, plant cells have doubling times or division rates measured in days, while this parameter in many microorganisms is in the order of minutes to hours. One of the fastest (and quite exceptional) doubling time recorded for a plant cell culture is

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15 h for tobacco cells (2). The doubling time (dt) can be calculated according to the following equation (7): dt =

ln2 m

where m represents the specific growth rate.

4. Notes 1. Volume of the cell package should be taken immediately after centrifugation, since sedimentation could alternate readings. 2. The conductivity of the culture medium can be determined using a digital conductivity meter or equivalent. 3. A very good linear correlation between the decrease in conductivity and the increase in dry weight can be found. References 1. Ryu DDY, Lee SO, Romani RJ (1990) Determination of growth rate for plant cell cultures: comparative studies. Biotechnol Bioeng 35:305–311 2. Fowler MW (1987) Products from plant cells. In: Bu’lok J, Kristiansen B (eds) Basic biotechnology. Academic, London, pp 525–544 3. Su WW (1995) Bioprocessing technology for plant cell suspension cultures. Appl Biochem Biotechnol 50:189–230 4. Fowler MW (1982) The large scale cultivation of plant cells. In: Bull MJ (ed) Progress in industrial microbiology, vol 16. Elsevier, Amsterdam, pp 207–229

5. González RC, Woods RE, Eddins SL (2002) Digital image processing using Matlab. Prentice Hall, London 6. Trejo-Tapia G, Arias-Castro C, RodríguezMendiola M (2003) Influence of the culture medium constituents and inoculum size on the accumulation of blue pigment and cell growth of Lavandula spica. Plant Cell Tissue Organ Cult 72:7–12 7. King PJ, Street HE (1977) Growth patterns in cell cultures. In: Street HE (ed) Botanical monographs, vol 11, Plant tissue and cell culture. Blackwell, Oxford

Chapter 5 Measurement of Cell Viability Lizbeth A. Castro-Concha, Rosa María Escobedo, and María de Lourdes Miranda-Ham Abstract An overview of the methods for assessing cell viability is presented. Different protocols of the most commonly used assays are described in detail so that the readers may be able to determine which assay is suitable for their own projects in plant biotechnology. Key words: Cell viability, Evans blue, Fluorescein diacetate, MTT, TTC, Tetrazolium salts, Pollen viability, Microspore viability

1. Introduction Plant cell cultures have been widely used as model systems for biochemical and physiological studies, as well as in some biotechnological processes, such as cell permeabilization, cell immobilization, or cell cultivation in bioreactors (1). A cell suspension can be defined by the number of single cells or aggregates that are dispersed in the culture medium; hence, its growth can be estimated by measuring either their biomass concentration in terms of fresh or dry matter per volume unit, or by cell density. Cell viability is a fundamental factor to consider since it is connected not only to the well-being of the culture but also to its productivity. Therefore, the accurate assessment of the number of viable cells in a population is very important to prevent the inclusion of low viable or dead cells in the calculations of results per cell or on a fresh weight basis or to indicate the maximal attainable cell density in production processes (2). A cell is considered viable if it has the ability to grow and develop (3, 4). Reagent-aided methods to assay viability are based on either the physical properties of viable cells, such as membrane integrity or cytoplasmic streaming, or on their metabolic activity, Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_5, © Springer Science+Business Media, LLC 2012

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such as reduction of tetrazolium salts or hydrolysis of fluorogenic substrates. To assess cell membrane integrity, dyes such as Evans blue (EB, (5, 6)), methylene blue (7), Trypan blue (8), neutral red (9), and phenosafranine (10) have been used. These compounds leak through the ruptured membranes and stain the contents of dead cells and then are accounted for via microscopic observation or spectrometric estimation. Other methods rely on the measurement of the activity of enzymes, such as reductases and esterases. In the case of reductases, both, MTT (3-[4,5-dimethylthiazol-2yl]-2,5-diphenyl tetrazolium bromide) and TTC (2,3,5-triphenyl tetrazolium chloride), accept electrons from the electron transport chain of the mitochondria; as a result, these molecules are converted to insoluble formazan within viable cells with fully active mitochondria (11). On the other hand, intracellular esterases hydrolyze a fluorogenic substrate (fluorescein diacetate) that can pass through the cell membrane, whereupon they cleave off the diacetate group producing the highly fluorescent product fluorescein. Fluorescein will accumulate in cells, which possess intact membranes, so the green fluorescence can be used as a marker of cell viability (12). An alternative method to measure the activity of esterases is the use of two-dimensional fluorescence spectroscopy, which eliminates the time-consuming, and often difficult, counting of viable and nonviable cells under the microscope (1). Nevertheless, images can now be easily obtained from the observed microscopic fields and then, they can be assessed with a number of computer programs that use functions or algorithms to discern the cells’ status, e.g., MATLAB, MathWorks Co. (13). Apart from the mentioned reagent-aided methods, there are also approaches for assessing cell growth and viability, which include typical on-line instruments based on capacitance (14), in situ dark field microscopy probe (15), infrared sensing (16), and turbidity (17), among others. In here, we present three different cases of study, in which the determination of viability was cumbersome to future efforts. 1. Cell death is an important feature to monitor during plant– pathogen interactions, so it must be measured accurately for the proper appraisal of the cellular responses. There have been contradictory reports of the measured cell viability in elicited cell suspension cultures (18–20). Hence, we have analyzed the elicitor induced cell viability changes in a tomato cell suspension using different methods. The use of the reduction of tetrazolium salts is proposed as a better indicator of metabolically active cells during the early hours of fungal elicitation (21); although, during the characterization of the cell suspension’s culture cycle, viability was monitored employing the Evans Blue assay. 2. Tissue immobilization in alginate is a suitable alternative in plant protocols for biochemical studies where the conservation

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of a complete differentiated state is pivotal. The use of alginate as the matrix of choice is based on its non toxicity to the tissues and its permeability to let nutrients in, and in turn allows the removal of debris or excretion compounds. We have developed a methodology for the establishment of an immobilized placental tissue culture from Capsicum chinense Jacq. with the aim of studying placental primary and secondary metabolisms. The use of a modification of Evans Blue assay (22) was proposed to assess the physiological state of this tissue. 3. Anther/pollen culture offers invaluable opportunities for the success of breeding programs, primarily through the production of homozygous lines. In order to efficiently exploit its potential, it is critical for pollen quality and their response frequencies to be as high as possible since further efforts are costly and labor intensive. Thus, reliable methods for testing pollen viability are essential, first in order to identify male sterility factors and subsequently to study environmental factors that affect its development in culture. Pollen viability of two species from the Capsicum genus: C. chinense Jacq. and C. annuum L. were evaluated to assess pollen grains’ ability to germinate in vitro (23). Additionally, the embryogenic response of uninucleated and binucleated microspores in media differing in the concentration of maltose and sucrose (24) was assessed using tetrazolium salts. Both MTT (25) and TTC offered a consistent approach to monitor the early response of multinucleated pre-embryo development in culture.

2. Materials 2.1. Cell Suspension Cultures

Calli were induced from young leaves of Solanum lycopersicum L. Var. Rio Grande on media with Murashige and Skoog (MS) salts (26) and supplemented with B5 vitamins (27), 3% (w/v) sucrose, 2.24 μM 2,4-dichlorophenoxyacetic acid, 0.049 μM kinetin, and 0.22% gelrite, pH 5.8.They were incubated in the dark at 25°C and subcultured every 3 weeks. Friable calli were transferred into 50 mL liquid medium (as previous, without gelrite) with orbital shaking (100 rpm). The cell suspensions were subcultured every 7 d by 1:5 dilution with fresh media. In order to observe an adequate response to the elicitor treatments, the number of cells in the suspension cultures was adjusted to 2.5 × 106 cells per mL (see Note 1).

2.2. MTT/TTC Assay

1. MTT stock solution: dissolve 50 mg in 10 mL sterile 50 mM phosphate buffer, pH 7.5 and store in the dark at 4°C. 2. TTC stock solution: dissolve 0.2 g in 10 mL sterile 50 mM phosphate buffer, pH 7.5 and store in the dark at 4°C.

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3. Sterile 50 mM phosphate buffer, pH 7.5. 4. 50% (v/v) methanol, containing 1% (w/v) sodium dodecyl sulfate (SDS). 2.3. Evans Blue Assay

1. EB stock solution 0.1%: dissolve 100 mg in 10 mL sterile water (10×) and store in the dark at 4°C. From this solution take 1 mL and dilute in 10 mL sterile water. 2. 50% (v/v) methanol, containing 1% (w/v) SDS.

2.4. Fluorescein Diacetate Assay

1. Fluorescein diacetate (FDA) stock solution: dissolve 25 mg of fluorescein diacetate in acetone. Preserve the solution in the dark at −20°C. 2. 50 mM phosphate buffer, pH 7.5.

2.5. Pollen Germination and Viability Assay

1. Germination media: 2 mM H3BO3, 2 mM Ca(NO3)2⋅4H2O, 2 mM MgSO4⋅7H2O, 1 mM KNO3, and 3% sucrose in distilled water. 2. Pollen viability stain [3% (w/v) aniline blue and 2% (w/v) basic fuchsin]: dissolve 150 mg of aniline blue and 100 mg of basic fuchsin in 5 mL of 25% (v/v) ethanol.

2.6. In Vitro Microspore Viability Assay Using MTT/TTC

1. MTT stock solution: dissolve 0.1 g in 10 mL of 3% (w/v) sucrose in sterile water and store in the dark at 4°C. 2. TTC stock solution: dissolve 0.2 g in 10 mL of 3% (w/v) sucrose in sterile water and store in the dark at 4°C.

3. Methods 3.1. MTT/TTC Assay (for Cell Suspension Cultures)

1. Wash aseptically tomato cell suspension samples (1 mL) with 50 mM phosphate buffer, pH 7.5. Repeat twice (see Note 1). 2. Resuspend the cells in 1 mL of the same buffer. 3. Add MTT or TTC to a final concentration of 1.25 or 2.5 mM, respectively. 4. Incubate samples for 8 h in the dark at 25°C. 5. Solubilize formazan salts with 1.5 mL 50% methanol, containing 1% SDS, at 60°C for a period of 30 min. 6. Centrifuge at 1,875 × g for 5 min and recover the supernatant. 7. Repeat steps 5 and 6. Pool the supernatants. 8. Quantify absorbance at 570 nm for MTT and 485 nm for TTC (see Note 2).

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1. Add EB stock solution to cell suspension samples (1 mL) to a final concentration of 0.025% (v/v). 2. Incubate for 15 min at room temperature. 3. Wash extensively with distilled water to remove excess and unbound dye. 4. Solubilize dye bound to dead cells in 50% (v/v) methanol with 1% (w/v) SDS at 60°C for 30 min. Repeat twice and pool the supernatants. 5. Centrifuge at 1,875 × g for 15 min. 6. Dilute the supernatant to a final volume of 7 mL. 7. Quantify absorbance at 600 nm (see Note 2).

3.3. Evans Blue Assay (for Immobilized Tissue Culture)

1. Add EB stock solution to immobilized placental tissue (1 g) to a final concentration of 0.042% (v/v). 2. Incubate for 45 min at room temperature. 3. Wash extensively with distilled water to remove excess and unbound dye. 4. Solubilize dye bound to dead cells in 50% (v/v) methanol with 1% (w/v) SDS at 60°C for 30 min. Repeat twice and pool the supernatants. 5. Dilute the supernatant to a final volume of 20 mL. 6. Quantify absorbance at 600 nm (see Note 3).

3.4. FDA Assay

1. Mix cell samples (1 mL) with 10 μL of FDA stock solution. 2. Incubate for 15 min at room temperature in the dark. 3. Adjust the volume to 4 mL with distilled water. 4. Centrifuge at 1,875 × g for 5 min. 5. Resuspend the pellet in 1 mL 50 mM phosphate buffer, pH 7.5. 6. Freeze quickly in liquid nitrogen. 7. Thaw and dilute samples to 3 mL with phosphate buffer. 8. Homogenize with a Brinkman polytron at high speed for 10 s. 9. Centrifuge at 1,875 × g for 20 min. 10. Dilute a 100 μL sample of the supernatant to a final volume of 2 mL. 11. Determine fluorescence at 516 nm, using a 492 nm excitation beam (see Note 2).

3.5. Microscopic Assay

1. Stain cell samples with FDA by mixing the samples (1 mL) with 10 μL of the stock solution. 2. Incubate for 15 min at room temperature in the dark.

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3. Wash with 50 mM phosphate buffer, pH 7.5. 4. Centrifuge at 1,875 × g for 5 min. 5. Resuspend in phosphate buffer (1 mL). 6. Counterstain with EB, following steps 1–5 but using 10 μL of the EB stock solution. 7. Determine the number of blue dead cells under a bright field and yellow-green fluorescent viable cells under ultraviolet light (excitation: BP 450–490 nm and emission: LP 520 nm) in an Axioplan microscope in ten randomized fields in a Sedgewick chamber. 3.6. Pollen Germination Assay

1. Collect anthers from newly opened pepper flowers between 8:00 and 11:30 am. 2. Dust the pollen of one dehiscent anther onto each 1.5-mL microcentrifuge tube. 3. Add 100 μL of germination media to each tube and gently invert them twice to obtain a homogeneous pollen suspension. 4. Transfer 25 μL of the pollen suspension to a clean cover glass so it spreads into a uniform film. 5. Invert carefully the cover glass on a clean glass slide without trapping air bubbles, and place the slices horizontally on a black moist humidity chamber at 25 ± 2°C for 24 h. 6. Monitor pollen germination with a stereoscope under dark field every 3–6 h for 24 h and record data for both germinated and nongerminated pollen. 7. Evaluate pollen viability for each time point using a dye solution containing 3% (w/v) aniline blue and 2% (w/v) basic fuchsin in 25% (v/v) ethanol. 8. Determine the percentage of germination at 3, 6, 12 and 24 h, using the following equation: % germination =

3.7. In Vitro Microspore Viability Assay Using MTT/TTC

total germinated pollen grains ´ 100. total pollen count

1. In all cases, aseptically collect anthers from in vitro cultures after 6, 12, 24, and 48 h, and 15 and 30 days of initiated the experiments, and put them in sterile 1.5-mL microcentrifuge tubes. 2. Liberate microspores in uni/binucleated and multicellular stage from the swollen anthers by mixing them with 1 mL of either 1% (w/v) MTT or 2% (w/v) TTC in 3% aqueous sucrose solution and incubate at 37°C for 24 h in the dark. 3. Transfer the immature pollen solution to a Sedgewick chamber and count 25 randomized fields using a light microscope (100× magnification) (see Note 4).

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4. Notes 1. Cell densities were determined by the chromium trioxide method. Briefly, 1-mL samples were taken at the indicated time and mixed thoroughly with 2 mL of 8% (w/v) chromium trioxide. Then, they were incubated for 15 min at 80°C. Onemilliliter samples were loaded on a Sedgewick Rafter counting cell chamber (London), which holds 100 mm3 and 10 randomized fields were counted twice per slide under bright light microscopy (10×). The mean and standard deviation of cell density values were calculated. 2. There was a robust correlation between enzyme activities and the number of viable cells employed in each assay (MTT, r 2 = 0.995; TTC, r 2 = 0.989; EB, r 2 = 0.979; FDA, r 2 = 0.996) and an internal control of heat-killed cells (75°C for 30 min) was used to estimate the percentages of relative viability (r 2 = 0.998). 3. In the case of immobilized placental tissue, an internal control of heat-killed tissue (100°C for 1.5 h) was used to estimate the percentage of relative viability. 4. Usually, five replicates from each sample were analyzed. Immature pollen was considered viable if it turned deep pink (MTT) or red (TTC), or it presented no color, but showed colored lines over its surface. References 1. Vanková R, Kuncová G, Opatmá J et al (2001) Two-dimensional fluorescence spectroscopy – a new tool for the determination of plant cell viability. Plant Cell Rep 20:41–47 2. Wei N, You J, Friehs K et al (2007) In situ dark field microscopy for on-line monitoring of yeast cultures. Biotechnol Lett 29:373–378 3. Palta JP, Levitt J, Stadeimann EJ (1978) Plant viability assay. Cryobiology 15:249–255 4. Pegg DE (1989) Viability assays for preserved cells, tissues and organs. Cryobiology 26: 212–231 5. Smith BA, Reider ML, Fletcher JS (1982) Relationship between vital staining and subculture growth during the senescence of plant tissue culture. Plant Physiol 70:1228–1230 6. Baker CJ, Mock MM (1994) An improved method for monitoring cell death in cell suspension and leaf disc assays using Evans blue. Plant Cell Tissue Organ Cult 39:7–12

7. Huang CN, Cornejo MJ, Bush DS et al (1986) Estimating viability of plant protoplasts using double and single staining. Protoplasma 135:80–87 8. Hou BH, Lin CG (1996) Rapid optimization of electroporation conditions for soybean and tomato suspension cultured cells. Plant Physiol 111(Suppl 2):166 9. Cripen RW, Perrier JL (1974) The use of neutral red and Evans blue for live-dead determinations of marine plankton. Stain Technol 49: 97–104 10. Wildholm JM (1972) The use of fluorescein diacetate and phenosafranine for determining viability of cultured plant cells. Stain Technol 47:189–194 11. Towill LE, Mazur P (1975) Studies on the reduction of 2,3,5- triphenyltetrazolium chloride as viability assay for plant tissue cultures. Can J Bot 53:1097–1102

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12. Moreira-Quiroz J, Valencia-Delgado V, ChávezBurbano P (2009) Implementación de un algoritmo para la detección y conteo de células en imágenes microscópicas. http://www.dspace. espol.edu.ec/handle/123456789/8375 . Accessed 30 Nov 2010 13. Steward N, Martin R, Engasser JM (1999) A new methodology for plant cell viability assessment using intracellular esterase activity. Plant Cell Rep 19:171–176 14. Carvell JP, Cannizzaro C (2007) On-line biomass monitoring in cell culture with scanning radio-frequency impedance spectroscopy. In: Smith R (ed) Cell technology for cell products. Springer, New York 15. Wei N, Flaschel E, Friehs K et al (2008) A machine vision system for non-invasive assessment of cell viability via dark field microscopy, wavelet feature selection and classification. BMC Bioinformatics 9:449–463 16. Kranner I, Kastberger G, Hartbauer M et al (2010) Noninvasive diagnosis of seed viability using infrared thermography. Proc Natl Acad Sci USA 107:3912–3917 17. Van Benthem R, de Grave W (2009) Turbidity sensor for bacterial growth measurements in spaceflight and simulated micro-gravity. Microgravity Sci Technol 21:349–356 18. Kodama M, Yoshida T, Otani H et al (1991) Effect of AL-toxin on viability of cultured tomato cells determined by the MTT colorimetric assay. In: Patil S (ed) Molecular strategies of pathogens and host plants. Springer, Berlin 19. Vera-Estrella R, Blumwald E, Higgins VJ (1992) Effects of specific elicitors of Cladosporium fulvum on tomato suspension

20.

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22.

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24.

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27.

cells. Evidence for the involvement of active oxygen species. Plant Physiol 99:1208–1215 Sánchez LM, Doke N, Kawakita K (1993) Elicitor induced chemiluminescence in cell suspension cultures of tomato, sweet pepper and tobacco plants and its inhibition by suppressors from Phytophthora spp. Plant Sci 88:141–148 Escobedo RM, Miranda-Ham ML (2003) Analysis of elicitor-induced cell viability changes in Lycopersicon esculentum Mill. suspension culture by different methods. In Vitro Cell Dev Biol Plant 39:236–239 Castro-Concha LA, Escobedo RM, MirandaHam ML (2006) Measurement of cell viability in in vitro cultures. In: Loyola-Vargas VM, Vázquez-Flota F (eds) Plant cell culture protocols. Humana, Totowa Rivera-Madrid R, Escobedo-GM RM, BalamGalera E et al (2006) Preliminary studies toward genetic improvement of annatto (Bixa orellana L). Sci Hortic 109:165–172 Dolcet-Sanjuan R, Claveria E, Huerta A (1997) Androgenesis in Capsicum annuum L.: effects of carbohydrate and carbon dioxide enrichment. J Am Soc Hort Sci 122:468–475 Rodríguez-Riano T, Dafni A (2000) A new procedure to asses pollen viability. Sex Plant Reprod 12:241–244 Murashige T, Skoog FA (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497 Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50: 151–158

Chapter 6 Pathogen and Biological Contamination Management in Plant Tissue Culture: Phytopathogens, Vitro Pathogens, and Vitro Pests Alan C. Cassells Abstract The ability to establish and grow plant cell, organ, and tissue cultures has been widely exploited for basic and applied research, and for the commercial production of plants (micro-propagation). Regardless of whether the application is for research or commerce, it is essential that the cultures be established in vitro free of biological contamination and be maintained as aseptic cultures during manipulation, growth, and storage. The risks from microbial contamination are spurious experimental results due to the effects of latent contaminants or losses of valuable experimental or commercial cultures. Much of the emphasis in culture contamination management historically focussed on the elimination of phytopathogens and the maintenance of cultures free from laboratory contamination by environmental bacteria, fungi (collectively referred to as “vitro pathogens”, i.e. pathogens or environmental micro-organisms which cause culture losses), and micro-arthropods (“vitro pests”). Microbial contamination of plant tissue cultures is due to the high nutrient availability in the almost universally used Murashige and Skoog (Physiol Plant 15:473–497, 1962) basal medium or variants of it. In recent years, it has been shown that many plants, especially perennials, are at least locally endophytically colonized intercellularly by bacteria. The latter, and intracellular pathogenic bacteria and viruses/viroids, may pass latently into culture and be spread horizontally and vertically in cultures. Growth of some potentially cultivable endophytes may be suppressed by the high salt and sugar content of the Murashige and Skoog basal medium and suboptimal temperatures for their growth in plant tissue growth rooms. The management of contamination in tissue culture involves three stages: disease screening (syn. disease indexing) of the stock plants with disease and endophyte elimination where detected; establishment and pathogen and contaminant screening of established initial cultures; observation, random sampling, and culture screening for micro-organism in multiplication and stored cultures. The increasing accessibility of both broad-spectrum and specific molecular diagnostics has resulted in advances in multiple pathogen and latent contaminant detection. The hazard analysis critical control point management strategy for tissue culture laboratories is underpinned by staff training in aseptic technique and good laboratory practice. Key words: Culture contamination, Endophytes, HACCP, In vitro contamination, Micro-propagation, Phytopathogens, Vitro pathogens

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_6, © Springer Science+Business Media, LLC 2012

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1. Introduction Plant cells, tissues, and organs are widely used in research, for example in the commercial production of plant metabolites, biotransformation of pharmaceuticals, production of proteins including antibiotics, plant genetic manipulation, and propagation of plants (1–4). In all applications, it is essential that the cultures and progeny plants be free of microbial contamination. Microbial contaminants, whether pathogens of the plant or not, may influence the behaviour of the tissues in vitro by releasing metabolites and proteins which affect the plant tissues and altering the composition and or pH of the culture medium. Furthermore, microbial contaminants may overrun the cultures resulting in the loss of valuable research material or cause production losses in micropropagation. If released in progeny plants, contaminants may spread disease locally and across international quarantine zones, resulting in crop loss and creation of potential reservoirs of inoculums for the pathogen. Progeny plants contaminated endophytically with nonpathogenic bacteria may also show adverse growth effects (5). Plant diseases have been described in classical literature, but it was not until the nineteenth century that plant pathology (syn. phytopathology) became an established discipline (6). An infrastructure for phytopathology has been established under the United Nations Food and Agriculture Organization (UN FAO; http://www.fao.org) with regional, inter-regional, national, and state agencies, professional bodies, local institutes, university and college departments, and commercial companies involved in disease research and development of diagnostics and diagnostic protocols (see for service providers: http://wdcm.nig.ac.jp/hpcc.html; http://www.rapidmicrobiology.com). This infrastructure is available to those working with plant cell, tissue, and organ cultures. Phytopathology services are available to plant tissue culturists for pathogen screening of stock plants, but tissue culturists also have to deal with some unique problems, namely, random endophytic contamination of stock plant tissues by environmental microorganisms and contamination of cultures by environmental micro-organisms and micro-arthropods (7–11). It is now widely accepted that most plants established from seed start life free of microbial contamination, that is, few diseases are vertically transmitted from generation to generation (12). Seed-derived plants may, however, be colonized epiphytically (externally) and perhaps endophytically by one or more environmental micro-organisms at/after planting. In contrast with seedderived plants, perennial crops and vegetatively propagated crops should, arguably, always be considered to be locally, if not systemically, endophytically contaminated (13, 14). These endophytes, in contrast with pathogens, are non-pathogenic strains of

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locally abundant micro-organisms (15), mainly bacteria, which enter through natural openings on the plant surface, or through wounds, or at sites of pathogen or pest damage. Many grow on plant tissue culture establishment media, but some may be suppressed by the high osmotic pressure of the media, specific media components, and pH of the media or not grow rapidly enough to be visible at the temperature of the culture and to be transmitted clonally in vitro and possibly overrun the tissues when the medium composition is changed, e.g. when the tissues are transferred to reduce strength medium for rooting, etc. (16). A further source of microbial contamination which is usually expressed rapidly is contamination by common environmental micro-organisms (bacterial and fungal) in the culture laboratory and growth room and by micro-arthropods in the latter (17). Inoculum of environmental micro-organisms is abundant universally but in some climates may show seasonal trends (18). While it is generally difficult, if not impossible, to recover heavily contaminated cultures, it may be possible to use antibiotics to treat slowgrowing contaminants (19). There is anecdotal evidence that some laboratories may be routinely using antibiotics to suppress microbial contaminants. In summary, the elements of pathogen, endophyte, laboratory, and growth-room contamination management depend on applying the principles of plant pathology, clinical microbiology, and Hazard Analysis Critical Control Point (HACCP) management (11, 20). Here, the application of these principles at each stage in the tissue culture (21) is discussed, namely, at Stage 0 (selection and preparation of stock plants); at Stage 1 (establishment of aseptic cultures in vitro); at Stage 2 (multiplication of cultures in vitro); and at Stage 3 (in vitro preparation of plants for return to the environment). Stage 4 (establishment of micro-plants extra vitrum) is not discussed here (see refs. 3, 16, 22).

2. Background: Pathogen and Microbial Plant Distribution in and on Plants

It is necessary to have an understanding of plant anatomy and the distribution of pathogens and other micro-organisms on and in plant tissues and organs to appreciate the background to the selection of plant parts for disease screening and the selection of tissues for culture (6). Plants propagated from certified seed (i.e. seed chemically treated with pesticides) or certified stock plants are free of specified pathogens but especially in the case of vegetative propagules may be contaminated with pathogens which have not been screened for, and endophytes. When the seed or vegetative propagule, e.g. aseptic micro-plant, is planted and germinates, it is colonized

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epiphytically by environmental micro-organisms. Microbial growth is abundant in the rhizosphere due to the high leakage of nutrients from plant roots (23). In root growth, the emergence of lateral roots creates openings in the root epidermis and cortex through which soil micro-organisms may enter, colonizing the intercellular spaces. Most such endophytic colonizers are excluded from the root core by the suberization of the exodermis (outer layer of cells around the vascular system) (24). Exceptions are soil-borne viruses which may become systemic (12). Beneficial micro-organisms which colonize root cells, such as mycorrhizal fungi and rhizobia, are not considered here as they are not a contamination issue (23). Some specialized pathogens (fungal vascular pathogens) have the ability also to enter the vascular system in the roots and systemically colonize the plant (6). Micro-organisms, including non-specialist root pathogens, that colonize the intercellular spaces of the root may be restricted at the root crown from moving up into the stem and colonizing the haulm (above ground) tissues (6, 25). The aerial parts of the plant are colonized by environmental micro-organisms and airborne pathogens, but the nutrient supply on the leaf surface is limited and other factors, such as water availability and UV exposure, may be highly variable (26). Foliar fungal and bacterial pathogens use pressure mechanism and/or enzymes to break down the plant structural barriers to colonization; usually, pathogen damage is easily seen by eye or magnifying hand lens and the affected tissues can be discarded for culture (6, 25). Insecttransmitted viruses/viroids and xylem- and phloem-restricted bacteria are injected into the vascular system and spread systemically therein. Some viruses are introduced into the parenchyma cells of the leaf and spread intracellularly via the plasmodesmata between the neighbouring cells and enter the vascular system from which they spread systemically (12). As plant tissues develop, intercellular spaces and cavities may develop which can be colonized by environmental bacteria entering through wounds and natural openings, such as leaf scars (24). These endophytes may increase cell leakage, providing plant nutrients for their colonization (6, 25). In general, where no organic manure is applied to the plant, the colonists are more likely to be from common plant surfacedwelling genera, such as Pseudomonas (14). In summary, plants can be colonized epiphytically and endophytically intracellularly and intercellularly by micro-organisms. Critically intracellular pathogens and presumably endophytes also, are usually restricted to the limit of development of the vascular system which develops back from the apex, and excluded from the solid tissues in the apex (12, 24): hence the basis of meristem culture for the elimination of pathogens and endophytes (16).

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It is important to observe the industrial maxim of “rubbish in, rubbish out” (referring to raw materials used in manufacturing) when approaching the establishment of tissue cultures. Every effort should be made to ensure that the stock plant(s) used is appropriately screened for pathogens of the crop and for endophytic contamination. Phytopathology databases, crop disease compendia (see http://www.apsnet.org for publications of the American Phytopathological Society, APS), should be consulted for information on disease of the crop and official protocols for the selection of mother plants and the production of pathogen-free stock (see http://fao.org; http://www.eppo.org; http://www.nappo.org). Note: Only officially approved screening methods are rigorous enough to satisfy official crop disease-certification schemes (27). Where the crop is not cultivated on a large scale, and this applies to many of the high-value crops which are micro-propagated, there may be no official methods published, but the general principles of guidelines for related species/genera and for the type of plant, e.g. woody ornamental, tuber crop, etc., should be observed (28). Selection of stock plants for tissue culture begins with the selection of vigorous, symptomless plants and their transfer to an insect-proofed greenhouse, where they are observed for disease symptoms and managed in a way which minimizes the risk of pathogen infection (21). Since expression of pathogen symptoms, especially virus symptoms, may be seasonal and/or nutritionally dependent, it is important to be familiar with the relevant plant pathology literature (6, 12); see also disease compendia of the APS at http://www.apsnet.org. It is also important to be aware that some viruses, viroids, and phloem/xylem-restricted bacteria may be symptomless but affect plant vigour (12). Indeed, some subliminal infections of plants, especially ornamentals, may be “beneficial”. Examples of beneficial infections are some flower breaks, notably the “Rembrandt” tulips, foliar variegations, and vein clearings (29). Also more than one virus may be present in a plant (12). Where more than one virus is present, the viruses may interact positively (giving severe symptom), negatively (reducing symptom severity), or not interact (12). It is important in multiple infections to confirm that all viruses have been eliminated. It is essential to reduce the risk of contamination spread between plants by sterilizing equipment before use on the next plant in the screening. Plants may be grown in Sunbags™, namely, plastic bags with bacterial filters which allow gaseous exchange with the ambient environment. Samples of the plants are taken for screening by grafting, enzyme-linked immunosorbent assay (ELISA), or nucleic acid (NA)-based diagnostics as prescribed in the official protocol or diagnostics producer’s instructions where

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applicable. Test results may be available in hours for ELISA to months in the case of grafting. Details of screening methods are given in Table 1. Should this official certification approach be impractical for a researcher, it may be possible to follow an alternative strategy based on the use of ELISA and NA-based diagnostics on the stock plant along with culture screening of the initial cultures (see Subheading 4). Testing for non-pathogenic endophytes is complicated by the random nature of contamination (13–15). As an aside, while the association between pathogens and their host plants is well studied, colonization by non-pathogenic endophytes is promiscuous and arguably influenced by random events, such as tissue damage and local inoculum pressure. There is insufficient evidence to date to support the hypothesis that some non-pathogenic endophytes are host specific. Methods used to screen for endophytes include expressing sap from the plant and culturing the extract on bacteriological media or surface sterilization of tissue pieces (explants) and their culture on bacteriological media (30, 31). The explants culture method may be more reliable as tannins and other plant materials released during sap preparation may inhibit growth of the endophyte (12, 16) in the preparation of sap samples for testing. 3.2. Methods for Pathogen and Endophyte Elimination from Stock Plants

Methods have been developed to eliminate specific viruses/viroids and intracellular bacteria from mother stock plants for the production of certified planting material for the grower (12, 32, 33). Heat therapy is widely used to eliminate plant viruses, and cold treatment has been used to eliminate some phytoplasmas (12, 16, 27). Thermotherapy is based on the destabilizing effects of heat on the pathogen. Plants are treated in “hot boxes” at temperatures in the range 32–40°C for 4–30 weeks. For species that are not heat tolerant, shorter periods at high temperature are alternated with ambient temperatures, e.g. 4–8 h at 40°C followed by 16–24 h at 20°C ( 16 ) . Virus elimination, as opposed to suppression, must be confirmed according to the FAO/regional organization’s protocols (see Subheading 2). The most widely used method to eliminate all classes of pathogens is “meristem culture” (4, 16). This depends on the hypothesis that micro-organisms affecting the plant do not penetrate the apical tissues (12) and are dependent on culturing the smallest apical tip that will survive in vitro on culture medium or when grafted to an in vitro micro-plant or aseptic seedling (16). This hypothesis generally holds up for most viruses and bacterial pathogens and it is not unreasonable to assume that it will also apply to (non-pathogenic) bacterial endophytes. The effective use of meristem culture depends on sterilization of the excised buds to eliminate surface contamination. Commonly, this is achieved by immersion in hypochlorite solution containing a surface-wetting agent. Hypochlorite is unstable and the active concentration should

Symptom expression

Widely used to identify pathogens

Widely used to identify pathogens

Widely used to identify pathogens

Widely used to identify pathogens

Microorganism

Viruses

Viroids

Bacteria

Fungi

Widely used to confirm pathogenicity and identify pathogen strains

Widely used to confirm pathogenicity and identify pathogen strains

Widely used to confirm pathogenicity and identify pathogen strains

Widely used to confirm pathogenicity and identify pathogen strains

Inoculation of indicator plants

Standard method used to identify viroid pathogens

Used to identify pathogens and environmental bacteria

Used to identify pathogens and environmental fungi

Not applicable

Not commonly used

Not commonly used

Not applicable

Not commonly used to identify plant pathogens; used to identify environmental and human pathogenic bacteria Commonly used for identification of environmental yeasts

Non-cultivable

Widely used to identify pathogens and environmental bacteria

Not commonly used

Light microscopy used to investigate morphology

Light microscopy used to investigate morphology

Widely used to identify viral pathogens

Not commonly used

ELISA is widely used to identify pathogens

Not applicable

Non-cultivable

DNA diagnostics

Electron microscopy used in research

Serological diagnostics

Biochemical tests

Microscopy

Culture on microbiological medium

Table 1 The main methods used to characterize pathogenic and non-pathogenic micro-organisms associated with plants

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be determined experimentally or commercial products used by their expiry date (34). George (16) recommends alternative surface sterilants for more intractable contamination. In meristem excision, the apical bud is surface sterilized and then dissected removing the outer leaflets/leaf primordia until the apical dome or apical dome plus first pair of leaf primordial is reached (4). This explant is then transferred to an appropriate meristem culture medium (16, 22). Menard et al. (35) recommend that the latter includes polyvinylpyrrolidone (PVP) to counteract the production of tannins which may block nutrient availability to the explants and suppress bacterial contamination of the explants and components of bacterial media to encourage the growth of bacterial contaminants. Early expression of bacterial contamination is critical to the prevention of the entry of contaminants into culture with consequential risk of contamination of established clean cultures during multiplication of cultures.

4. Stage 1: Screening of Initial Cultures 4.1. Screening of Initial Cultures of Large-Scale Production Crops

Assuming that pathogen-free stock is available, then the focus is on screening for the presence of latent bacterial endophytic contamination or environmental contamination introduced during the tissue culture process (Fig. 1). In most cases, plants are introduced into culture via meristem culture; however, in some cases, other explants are used, namely, nodes, internodes, leaf and stem explants, and rarely root tissues (16, 22). In contrast to meristem culture, establishment of tissue cultures via other explants posed the high risk of transmission by inter- and intracellular micro-organisms present in those explants. The risk of introduction of contamination with root explants is so great that the latter explants are rarely used to establish cultures (16, 22). Commonly, cultures are only visually inspected for contamination assuming that any bacterial contamination will be expressed, that is, the bacteria will grow on the plant tissue culture medium. This is not an unreasonable assumption but is not universally applicable as some endophytic bacteria may be inhibited by the high salt, pH, and/or plant growth regulators in the culture medium or may not grow rapidly at the culture temperature (35). For temperate crops, it is likely that bacterial endophytes and environmental microbial contaminants will grow at the growth-room temperature of 20–25°C, but bacterial endophytic contaminants of tropical crops may have higher temperature optima. Since most laboratory contaminants and endophytes may be common environmental micro-organisms, they are likely not to be fastidious with respect to the components of their culture and may grow on common bacteriological media. This also applies to yeast endophytes and the media used in screening should

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Fig. 1. A scheme illustrating a two-phase strategy for managing contamination in tissue culture, where the focus is on pathogen screening and pathogen and contaminant elimination before or at the establishment of the cultures, and good laboratory working practice is used to exclude environmental organisms during the in vitro stages. It is hypothesized that most pathogens and endophytes are eliminated if cultures are established from meristem explants, but this must be confirmed by screening of the initial cultures.

reflect possible contamination with the latter. The minimum screening conditions should be based on plating the excised base of the established explants on broad-spectrum (“universal”) bacterial and yeast diagnostic media (see http://www.sigma.com for media formulations) and followed by incubation at 20, 25, and 30°C for approx. 10 days. Cultures may be contaminated also by airborne fungal spores of, e.g., Penicillium and Aspergillus spp. These rapidly grow on plant tissue culture media and can be identified using a light microscope (36) (Fig. 2). If pathogen-free stock is unavailable and meristem culture is being used to eliminate pathogens and subliminal endophytes, then the complexity of screening is increased, especially where the cultures will be used to multiply pathogen-free stock for certification as free of specific pathogens. This is because the official certification schemes generally involve screening based on greenhouse/ field-grown plants (27), that is, screening is not accepted for in vitro cultures and progeny plants must be established and grown in vivo before testing can be carried out. In the case of fruit trees, the classic screening for some pathogens involves grafting to rootstock of indicator species (27). In some areas, micro-propagators

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Fig. 2. A flow diagram showing the stages in micro-propagation. Representative micro-organisms, which indicate failure of aseptic technique and equipment at the respective stages, are given.

can obtain cultures established from health-certified mother plants provided by the quarantine authorities. The latter “certified cultures” may, however, only be subcultured for a specified number of generations or have a time limit before their certified status expires and they must be replaced by fresh cultures (9).

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4.2. Screening of Minor Crops and Species of Research Interest

Commonly, micro-propagators and researchers are supplied by clients or select themselves plants for research, species for which no official disease-screening protocols exist, implying that disease risks may be unknown or poorly characterized, albeit the disease risk for wild or weakly domesticated plants is less than that for highly bred agricultural and horticultural crop varieties (37). The micro-propagation client may request that the tissue culture progenies are free of a specified pathogen. However, for researchers, there is the risk that latent contaminants may influence experimental results (38), whereas for micro-propagators there is the risk of significant commercial losses in production and even a “nonpathogenic” endophyte when present in micro-plants from establishment may cause losses in the field (5). If a pathogen is specified by the micro-propagation client, the normal approach is to use a commercially available ELISA or NA-based test to screen the mother plant(s) in vivo or the established cultures in vitro. The cultures should also be screened for endophyte contamination. Screening of cultures poses special problems (see Subheading 2).

4.3. Contamination in Externally Sourced Mother Cultures

It is important to note that cultures obtained from official sources, such as state laboratories and international germbanks (http:// www.bioversityinternational.org; http://www.cgiar.org), may be certified free of specified pathogens but may not be free of endophytes which can overrun the cultures when subcultured to a different medium. In some cases, mother cultures bought in from external sources may have been grown on antibiotics to suppress endophytes. If antibiotics are present in the medium, the externally sourced cultures may express microbial contamination when transferred to antibiotic-free media in the laboratory. It is important to test a sample of externally sourced cultures as a precaution. Explants should be incubated on antibiotic-free media as for screening of cultures for endophytes above (Subheading 3.2). There are anecdotal claims of the beneficial growth effects of some microbial contaminants of tissue cultures (39). This may be explained by the effects of these micro-organisms on the pH of the medium, by their enhancement of nutrient availability to the cultures, or by their production of plant growth regulators (40, 41). Any such positive growth effects must be offset against the potential risks of culture losses when the medium is altered or damage to the progeny plants at and after establishment occurs.

4.4. Action to Be Taken When Contamination Is Detected in Stage 1 Cultures

If contamination of the initial explants by fast-growing cultivable contaminants is detected, there are two possibilities: firstly, the stock plants may be treated with appropriate antibiotics to suppress the contaminant in the stock plant and cultures may be established from new growth in the stock plants (42); secondly, if the contaminant is fastidious, or slow growing, an attempt to eliminate the contaminant from the cultures may be made by inclusion of

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antibiotics in the culture medium (43). It is important to recognize that antibiotics may be bacteriostatic rather than bacteriocidal and may be toxic to the plant cultures (44, 45), and consequently only new growth should be excised and subcultured. Antibiotics and antibiotic cocktails have been used empirically by many plant tissue culturists (19). Regardless of which antibiotic strategy is used, that is, antibiotic treatment of the stock plant or incorporation of antibiotic into the culture medium, the cultures must be re-screened to confirm elimination of the contaminant before subculture. Correct bacterial identification procedure for antibiotic screening/identification involves isolation in pure culture (by streak plating), establishment of single-colony cultures (30), and screening for antibiotic sensitivity on diagnostic sensitivity testing (DST) medium (43). Antibiotics are incorporated into the plant tissue culture medium at two to four times the minimum inhibitory concentration and testing should be carried out to confirm that their action is not inhibited by components of the plant culture medium (43). Antibiotics which are potential mutagens should not be used (46). Also only early-generation antibiotics should be used to avoid the risk of selection for antibiotic resistance in the culture. If virus or viroid contamination is present in the cultures, the antiviral chemical ribavirin (syn. Virazole; 1-β-D-ribofuranosyl-1, 2, 4-triazole-3-carboxamide) may be incorporated into the culture medium (12, 47, 48). Ribavirin is virustatic and as with antibiotics, only new tissue should be excised for subculture and screening (47). It has been reported that ribavirin interacts with cytokinins and it may be the best to either reduce or eliminate cytokinin in the elimination medium (49). Confirmation of virus elimination should be confirmed by inoculation of the appropriate indicator plant (see Subheading 5.3).

5. Screening Methods 5.1. Infrastructure for Plant Pathology

As referred to in Subheading 1, there is a comprehensive infrastructure in plant pathology. The international phytosanitary regulatory authority is the Food and Agriculture Organization of the United Nations (http://www.fao.org). This is supported by regional organizations—the North American Plant Protection Organization (http://www.nappo.org), the European and Mediterranean Plant Protection Organization (http://www.eppo.org), with other regional organizations (see http://www.fao.org for further information). The APS (http://www.apsnet.org) has an international supporting role in publishing crop disease compendia and details of new diagnostic methods. Working groups of the International Society for Horticultural Science (http://www.ishs.org) and of other plant pathology societies contribute also to the

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development of new methods of disease diagnosis. There are also governmental organizations and private companies which supply mother cultures, plant disease diagnostics, and disease diagnosis. 5.2. Classical Methods for Pathogen Screening of Plants

The general focus in screening plants is on the detection of viruses, viroids, and fastidious or non-cultivable bacterial pathogens. Historically, viruses and viroids were detected by sap, vector, dodder, or graft transmission to indicator plants (12, 50) while intracellular, generally fastidious, or non-cultivable bacterial pathogens were detected by graft or dodder transmission to indicator plants (32). Indicator plants are species/genotypes which show a specific reaction to inoculation with a specific pathogen or pathogen strain (51). These transmission-based tests were slow and required the maintenance of an array of indicator plants at the appropriate growth stage for the test. For details of the classical methods, see Noordam ((51); Table 1).

5.3. Molecular Plant Diagnostics

Classical transmission tests have been largely superseded by antibody-based methods, principally ELISA (52) or nucleic acid-based molecular diagnostics for virus, viroid, and mollicute (fastidious/ non-cultivable xylem- and phloem-restricted bacteria) detection (33, 53, 54). Classical detection/colony identification of cultivable bacterial plant pathogens is based on growth response/characteristics on differential or selective media (30, 31) and to a limited extent on fatty acid profiling (55). ELISA and NA-based diagnostics have two common features: a specific binding function and a signal amplification function. These functions provide the specificity and sensitivity of the test. In virus antibody tests, the antibody is raised against viral coat protein determinants, where there may be one or many determinants per coat protein. The uniqueness of the determinant(s) to the specific viral coat protein determines the specificity of the ELISA (or other antibody-based tests). ELISA may be based on “monoclonal” or “polyclonal” antibodies to achieve different levels of specificity (56). The sensitivity of ELISA is based on the enzyme–antibodylinked activity on the chromogenic substrate used in the test (52). An important consideration in the interpretation of ELISA results, which are statistical positives/negatives, is to have an appropriate positive/negative threshold (57). The highly conserved proteins involved in virus replication are in low relative abundance, difficult to harvest free of host protein contamination, and, hence, not used commercially in ELISA kits. ELISA is of limited use in identifying bacterial plant pathogens as the available determinants, e.g. membrane and flagellar proteins, may not discriminate between pathogenic and non-pathogenic isolates. In general, while a positive ELISA test, taken in conjunction with disease symptom expression, is taken as a positive pathogen diagnosis, it is advisable that appropriate test (indicator) plants are inoculated with the isolated

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micro-organism to confirm pathogenicity. It is important to confirm Koch’s Postulates for cultivable micro-organisms (6). Unlike ELISA, antibodies for which cannot be raised against non-transcribed regions and highly conserved regions of the viral genome, NA probes can be synthesized to detect all regions of the genome (58). Conserved and hypervariable regions of plant viral genomes have been identified and probes can be designed to give narrow- or broad-spectrum detection/identification (12). NA probes are routinely used for the detection of viroids which lack protein coats. NA probes are also used to detect the presence of bacteria; commonly, probes against conserved regions of the ribosomal 16S ribosomal DNA may be used to detect the presence of any/all bacteria, whereas probes against hypervariable regions of 16S rDNA gene can be used to discriminate bacteria to the species and subspecies levels (58). There are various methods of enhancing and detecting NA-probe signals. In the case of plant viruses (most have RNA genomes) where RNA probes are used, the sequence is converted to a DNA copy by reverse transcriptase and then amplified by DNA transcriptase. In the case of bacterial detection, DNA probes are amplified by DNA transcriptase (59). The amplified sequence may be detected by separation on gels and visualized by silver staining, or the probe may be fluorochrome labelled and viewed in liquid (60). DNA micro-arrays may be used to screen for multiple organisms in a sap or tissue extract (58, 61, 62). 5.4. Screening of Plants for Bacterial Endophytes

6. Stages 1, 2, and 3: Laboratory and Growth-Room Contamination Management

Miniature biochemical test kits (http://www.biomerieux.fr; http:// www.oxoid.com) and growth on differential or selective media are used widely to identify environmental and human pathogenic bacteria and can be used to detect/identify the latter associated with plants as endophytes ((63, 64); Table 1). For suppliers of media, etc., see http://www.sigmaaldrich.com and http://www.oxoid.com. Moreover, NA probes offer the possibility of detecting any contamination by bacteria of a tissue which is critically what is required in screening for promiscuous/random bacterial contamination. For this purpose, probes against the conserved regions of the 16S rDNA gene are used to screen for bacterial presence, as opposed to probes against the variable regions of the 16S rDNA gene used to develop more specific probes (58, 59).

As discussed above, when axenic, perhaps more precisely “aseptic”, cultures have been achieved, the challenge is to prevent re-contamination in the laboratory (Figs. 1 and 2). While there may be overlap in the species which constitute “pathogens”, “endophytes”, and “environmental micro-organism” (see above), laboratory

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contaminants are generally non-fastidious airborne fungi and bacteria that are fast growing and rapidly overrun cultures and are uncurable with antibiotics. Control is based on excluding them from the laboratory environment and cultures by good HACCP management. 6.1. Personnel Training

It is important that all personnel working in or sharing common facilities with the tissue culturists are trained in aseptic technique and have a basic understanding of microbiology. The most important aspects are control of sources of contamination and prevention of contamination of the cultures in the culture laboratory and growth rooms. Training can be provided by digital media (http:// www.sigmaaldrich.com/life-science/cell-culture/learning-center/ cell-culture-videos.html) and can be re-enforced by visits to hospital laboratories and food processing companies which share common contamination management principles. It is important that personnel are familiar with the need to avoid contamination from the external environment which involves removing outdoor shoes before entering the work area or putting on disposable overshoes; wearing of laboratory coats which should be regularly laundered; removal of items of jewellery; washing of hands with aseptic washes; and wearing of disposable headgear. Tissue culture personnel should also be trained in aseptic laboratory technique from correct autoclaving procedure to cleaning and maintenance of sterile transfer cabinets and use of dissection equipment and laminar flow cabinets. Important aspects of operations in the laminar flow cabinet are that nothing should be placed between the operative and the laminar air source; dissection should be carried out on a sterile tile or similar, which focuses attention on the need to maintain a sterile working surface and avoids cutting the surface of the cabinet; and instruments should be sterilized between each distinct culture event. The use of equipment is discussed further below. It is important that all personnel be on the look out for sources of contamination at all times. Contaminated cultures, whether detected in the growth room or at subculture, should be autoclaved unopened and subsequently disposed of. Cultures before subculture should be examined carefully for signs of contamination. Contaminated cultures should be autoclaved unopened prior to disposal. If testing for latent endophytes in initial material and brought-in cultures has been carried out, the main contamination risk is from environmental micro-organisms which are generally expressed on plant culture media, and the occasional risk of humanassociated micro-organisms (bacteria and yeasts) also probably expressed on plant culture media (14, 64, 65). Personnel with infectious bacterial or yeast diseases (67) should desist from working in the tissue culture laboratory until they have recovered. An important feature of laboratory contamination is the change over

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time in culture, predominantly from contamination with plantassociated bacteria to mixed contamination with human-associated bacteria and yeasts (68). 6.2. Maintenance of Laboratory Equipment 6.2.1. Laboratory and Growth-Room Design

Many of the problems associated with laboratory and growth-room contamination can be resolved by good laboratory design or modification, primarily aimed at preventing the entry of environmental micro-organisms. Key aspects are entry airlocks, provision of areas for the personnel to wash and change into laboratory clothing, and filtering of inputs such as water and air into the laboratory. While growth-room shelving may be solid to allow water circulation for bottom cooling of the cultures, it is generally of open mesh to allow air circulation (16). Open-mesh shelving can allow microarthropods to drop down from infected cultures on upper shelves to contaminate healthy lower cultures. Where micro-arthropod contamination is detected, plastic or other sheeting should be, at least temporarily, placed on the shelves to prevent this occurrence. For more information on micro-propagation laboratory design, see ref. 69.

6.2.2. Water Supply

In some regions, potable and generally non-potable water may carry heavy microbial contamination and may have a high salt content. It may be desirable to use a UV-water sterilizer or water filtration unit to purify the water entering the laboratory. If used, online water filtration equipment must be maintained in line with the manufacturers’ recommendations and under local conditions. Only filtered, single-distilled or double-distilled water should be used for preparing media (16).

6.2.3. Culture Vessels

The problem of microbial contamination of cultures in the growth room can be influenced by the type of culture vessel lid or closure used (16). Cultures need gaseous exchange with the ambient atmosphere to allow oxygen and carbon dioxide exchange and escape of ethylene and other volatiles (70, 71). To achieve gaseous exchange, culture vessels with loose lids are commonly used (Petri dishes, food jars, and customized plant tissue culture vessels) in plant tissue culture (16). The problem with most types of vessel closures (lids) is that while allowing gaseous exchange they also allow spores and micro-arthropods access to the cultures. The medium may also dry out, i.e. the osmotic pressure increases which can suppress the growth of some microbial contaminants and affect the tissue growth. Also, spores and micro-arthropods may be sucked into the vessels at the end of the light period when the atmosphere in the vessels cools and creates a negative pressure in the vessel. It has been shown that plastic packaging materials allow gaseous exchange while preventing microbial/micro-arthropod contamination (72). It is now a common practice in micropropagation laboratories to wrap conventional culture vessels in “cling film”-type materials (the gaseous permeability of the material

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should be checked or advice obtained from the manufacturer) to control growth-room contamination. Culture vessels are commonly adapted glass food jars and are recycled. Medium is dispensed into the jar which is sterilized by autoclaving. Alternatively, food plastic containers or dedicated plastic tissue culture containers are used (http://www. sigmaaldrich.com). The former may not withstand autoclaving but may be sterile as a consequence of the thermal-moulding process used in their manufacture or may be sterilized by gamma irradiation. Pre-sterilized medium is dispensed into these vessels in the laminar flow cabinet. 6.2.4. Autoclaves

Media/equipment/instruments that are autoclaved should always be accompanied by (autoclave) tape which provides an indicator when the appropriate conditions (121°C and 1.05 kg/cm3) have been reached inside the autoclave. Small volumes of media dispensed into culture vessels require 15 min under standard conditions for sterilization, but bulk sterilization of media requires a pre-heating period to allow the medium to reach 121°C (see ref. 16 for information of sterilization times for large volumes of liquid). Vessels should not be tightly lidded during autoclaving to satisfy the conditions for sterilization. Heat-labile materials should not be autoclaved but instead sterilized by ultrafiltration (16). It is a good practice to rest autoclaved medium for a few days before use to allow any bacterial contamination which passed through autoclaving to be expressed. In general, contamination in solid media is seen as fungal mycelium “ball” development and/or bacterial colony development in, as opposed to on, the surface of the medium (see below). Instruments should be sterilized individually or in sets as opposed to batches to avoid re-contamination when instruments are selected for use.

6.2.5. Automated Medium Dispensers

Equipment for the automated dispensing of medium into Petri dishes is widely used in clinical laboratories. The medium sterilization and peristaltic pump functions of this equipment are used in micro-propagation laboratories, where large volumes of media are used. As above, media should be poured a few days in advance of use and monitored for signs of bacterial/fungal contamination. Contamination on the surface of the poured medium indicates faulty dispensing equipment or procedure. As with other laboratory equipment, the item should be routinely serviced.

6.2.6. Laminar Flow Cabinets

The laminar flow cabinet is designed to provide a positive clean air pressure space for aseptic operations. This is achieved by passing the air through a course pre-filter followed by an HEPA filter which removes microbial spores (16). The pre-filter should be removed and washed regularly. Similarly, the HEPA filter should be replaced as recommended by the manufacturers. It should not be assumed that the HEPA filter is functioning. Correct functioning can be

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tested by using an airflow meter, and by placing open media plates in the cabinet workspace and by sealing these and incubating them for 3–7 days at 25°C to observe any microbial growth. It is important that the workspace be cleaned before using a laminar flow cabinet. This can be done by incorporation of a germicidal UV lamp in the cabinet (making sure that the sides of the chamber are not damaged by UV—Perspex sides should be replaced by toughened glass), by covering when not in use, the opening of the chamber with a blind, and/or by swabbing all the interior space with commercial antimicrobial solution. The cabinet should be turned on for a “warm-up” period before use. For a training video, see http://www.sigmaaldrich.com/life-science/cell-culture/ learning-center/cell-culture-videos.html; see also ref. 16. 6.2.7. Instrument Sterilization in the Laminar Flow Cabinet

There are several methods used to sterile dissecting instruments during use in a tissue culture session. Traditionally, flame sterilization in ethanol was used, but this method can result in accidental fires and injury to personnel. Alternative methods are the use of hot air guns and hot bead sterilizers (http://www.sigmaaldrich.com).

6.2.8. Laboratory and Growth-Room Atmosphere

The laboratory atmosphere can become contaminated, sometimes seasonally, by atmospheric spores of yeasts, fungi, and bacteria (18). The main inoculum entry points are the access doors and open windows. The problem can be addressed by providing an entry air lock to the laboratory and creating a positive pressure in the laboratory. Advice should be sought from appropriate hospital laboratory designers/constructors. It is also advisable to sample the laboratory/growth-room atmosphere and inspect and screen the cultures in the growth room for contamination regularly, especially slow-growth (long-term storage) cultures which may become reservoirs of infection. Chemical sterilization of the laboratory/ growth rooms can be carried out by experts, but this may shut down activities for a period of time.

7. Management of MicroPropagation Facilities

Depending on the scale of operation, it may be necessary to allocate the contamination management function to one or more of the personnel. Management should be formally structured and based on HACCP analysis as used in the food industry (11, 20). The focus in HACCP is on staff training and equipment servicing, health/contamination status of the mother plants, screening of the initial cultures, sampling and screening of samples of subcultures, and monitoring of the growth rooms for micro-arthropod, bacterial, and fungal contamination. Biomarkers of contamination associated with the stages in tissue culture are shown in Fig. 2. The characteristics of these biomarkers are given in Table 2.

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Table 2 Characteristics of HCCP biomarkers of plant tissue cultures Indicator organism

Type

Characteristics

Quick test

Pseudomonas fluorescens

Eubacteriaceae

Gram-negative, motile rods that oxidize glucose

(31)

Erwinia spp.

Eubacteriaceae

Gram-negative, motile more than 4 peritrichous flagellae, grows anaerobically

(31)

Klebsiella spp.

Eubacteriaceae

Serratia spp.

Eubacteriaceae

(31) Gram-negative, motile rods, highly mucoid colonies, produces red pigment, facultative anaerobes, oxidase negative, nitrate positive

api 20Ea

Agrobacterium Eubacteriaceae spp.

Gram-negative, motile, non-spore-forming rods, grows on D-1 medium

(31)

Bacillus spp.

Eubacteriaceae

Gram-positive, motile rods; produces large, grey–white colonies with irregular margins on blood agar; produces endospores when stressed; motile/non-motile; catalase positive

(31)

Rhodotorula spp.

Basidiomycetes

Unicellular (blasto-)conida globose to elongate which may be encapsulated; pseudohyphae are absent or rudimentary; colonies cream to pink, coral red, orange, or yellow in colour

api 20C AUXa

Penicillium spp.

Deuteromycetes

Conidiophores arising from the mycelium singly or less commonly in groups or fused, branched near the apex, ending in spore-producing cells; the spores are produced sequentially and form chains

(36)

Staphylococcus spp.

Eubacteriaceae

Gram positive, non-motile, spherical in clusters, anaerobic fermentation of glucose with acid production, catalase, nitrate and coagulase positive

api STAPHa

Streptococcus spp.

Eubacteriaceae

Gram positive, non-motile, spherical in chains, aerobic action on glucose, catalase negative

api STREPa

Candida albicans

Saccharomycetales Produces blastospores, pseudohyphae, and chlamydospores on cornmeal Tween 80 agar at 25°C after 72 h

api ID32Ca

For a complete list of commercial diagnostic suppliers for bacterial and yeast biochemical detection kits and media see http://www.rapidmicrobiology.com, http://www.sigmaaldrich.com, and ahttp://www.biomerieux.com

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8. Conclusions In recent years, several developments have influenced how disease and pathogen contamination is approached and managed. Firstly, there has been the recognition that endophytic contamination of perennial/vegetatively propagated plants is possibly widespread (13, 14). These contaminants are non-pathogenic to the stock plant, are intercellular, may be locally distributed, and are potentially cultivable on common microbial media. Some endophytes may be potentially pathogenic to the stock plants depending on the development of a quorum to initiate pathogenesis (73). They may enter initial cultures (Stage 1) in explants subliminally, and if suppressed by components of the plant tissue culture medium or culture environment, they may spread at subculture to emerge when the medium concentration is altered for culture multiplication (Stage 2) or root induction in vitro (Stage 3), overrunning the cultures and causing extensive economic losses, especially in micropropagation and large-scale industrial plant cell culture (74). Bacterial intercellular endophytes are sometimes regarded as potentially beneficial micro-organisms (39). Such contaminants, however, while posing a direct threat of vitro pathogenicity may also cause disease in the progeny plants (5). This difference in behaviour may be that in the stock plants the distribution is localized, whereas in the progeny plants the contaminant may become systemic in the “softer” tissues (21). Secondly, developments in molecular diagnostics, especially in NA-based diagnostic, have made available the possibility of probes which are of broad spectrum and can detect generically bacteria, fungi, fungal-like micro-organisms, virus families, and virus-like micro-organisms (53, 58). While ELISA has the potential to detect virus strains and some plant viral families, developments in NA diagnostics have greater potential and, when used in micro-arrays, have the potential to screen for all the pathogens of a crop in a single test (58, 61, 62). It takes time to adapt experimental protocols for commercial application, and availability then is dependent on the market demand. Nevertheless, one can be optimistic that methodological advances will continue to become available to plant tissue culturists directly or via their service providers. Plant disease diagnosticians are seeking rapid sensitive tests that will eliminate the need to inoculate indicator plants to confirm pathogenicity, whereas the plant tissue culturists are also seeking a universal test for the detection of latent bacterial endophyte contamination. Thirdly, there have been a few reports of the transmission of human pathogenic bacteria via tissue cultures to infect personnel during subculture (66). It is unclear if plants infected with human pathogens or plant biocontrol bacteria related to human pathogenic

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bacteria (75) pose a threat to purchasers, e.g. when introduced into hospitals and other location housing immune-compromised patients. Fourthly, the commercial development of plant diagnostics and provision of diagnostic services enable outsourcing of pathogen identification and detection of endophyte contamination, where the expertise is not available within the laboratory. There are many companies and state laboratories operating internationally, offering services to research and commercial laboratories. It is also easier now for micro-propagation companies and researchers to identify laboratories working on specific diseases or diagnostics using Google Scholar (http://scholar.google.com), JSTOT (http://www.jstor.org), or, if access is available, the Web of Science (http://www.isiwebofknowledge.com) or journal publishers Web sites such as Science Direct (http://www.sciencedirect.com). Thus, the prohibitive cost of developing and validating diagnostics may be defrayed. Fifthly, international germplasm collections (germbanks) (http://www.bioversityinternational.org; http://www.cgiar.org), botanic gardens (International Union of Biological Sciences, IUBS; http://www.iubs.org), and commercial sources may be able to supply mother cultures from their collections or from a client’s material. But a caution: Unless certified, the cultures may not be free of pathogens and/or endophytes and/or they may have incorporated an antibiotic in the medium to suppress bacterial contamination. Externally sourced culture must be rigorously indexed for pathogens and endophytes unless the supplier will undertake to indemnify the client against consequential losses. In summary, the anticipated further development of broadspectrum NA-based diagnostics implies that it will be possible in the future to be confident that initial cultures are not only aseptic but also axenic and can be certified (76). However, during subculture, there will remain the risk of microbial contamination. To avoid the latter, the principles of HACCP-based management as outlined above should be followed. References 1. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15: 473–497 2. Stafford A, Warren G (1991) Plant cell and tissue culture. Open University, Milton Keynes 3. Pierik RL (1999) In vitro culture of higher plants. Kluwer, Dordrecht 4. Trigiano RN, Gray DJ (2010) Plant tissue culture, development, and biotechnology. Taylor & Francis, New York

5. Long RD, Curtin TF, Cassells AC (1988) An investigation of the effects of bacterial contaminants on potato nodal cultures. Acta Hortic 225:83–92 6. Agrios GN (2004) Plant pathology, 5th edn. Academic, London 7. Krantz GW (1978) A manual of acarolgy. Oregon State University, Corvallis 8. Cassells AC (1985) Bacteria and bacteria-like contamination of plant tissue cultures. ISHS, Wageningen

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9. Cassells AC (1997) Pathogen and microbial contamination management in micropropagation. Kluwer, Dordrecht 10. Cassells AC, Doyle BM, Curry RF (2000) Methods and markers for quality assurance in micropropagation. ISHS, Leuven 11. Leifert C, Cassells AC (2001) Microbial hazards in plant tissue and cell cultures. In Vitro Cell Dev Biol Plant 37:133–138 12. Hull R (2001) Matthew’s plant virology. Academic, New York 13. Bacon CW, White JF Jr (2000) Microbial endophytes. CRC, Roca Baton 14. Tyler HL, Triplett EW (2008) Plants as habitat for beneficial and/or human pathogenic bacteria. Annu Rev Phytopathol 46:53–73 15. Cassells AC, Tahmatsidou V (1997) The influence of local plant growth conditions on nonfastidious bacterial contamination of meristem-tips of Hydrangea cultured in vitro. Plant Cell Tissue Organ Cult 47:15–26 16. George EF (1993) Plant propagation by tissue culture part 1 – the technology. Exegetics, Basingstoke 17. Pype J, Everaert K, Debergh PC (1997) Contamination by micro-arthropods. In: Cassells AC (ed) Pathogen and microbial contamination management in micropropagation. Kluwer, Dordrecht, pp 259–266 18. Gregory PH (1973) The microbiology of atmosphere. Leonard Hill, Aylesbury 19. Reed BM, Tanprasert P (1995) Detection and control of bacterial contaminants of plant tissue cultures: a review of recent literature. Plant Tissue Cult Biotechnol 1:137–142 20. Wallace C, Mortimore S (2009) HACCP: a practical approach, 2nd edn. Springer, New York 21. Debergh P, Maene L (1985) Some aspects of stock plant preparation for tissue culture propagation. Acta Hortic 166:21–23 22. George EF (1996) Plant propagation by tissue culture part 2 – in practice. Exegetics, Basingstoke 23. Mukerji KG, Singh J, Manoharachary C (2010) Microbial activity in the rhizosphere. Springer, New York 24. Mauseth JD (2008) Plant anatomy. Blackburn, Caldwell 25. Strange R (2003) Introduction to plant pathology. Wiley, New York 26. Andrews JH, Harris RF (2000) The ecology and biogeography of microorganisms on plant surfaces. Annu Rev Phytopathol 38: 145–180 27. Hadidi A, Khetarpal RK, Koganezawa H (1998) Plant virus disease control. APS, St Louis

28. Krczal G (1998) Virus certification of ornamental plants – the European strategy. In: Hadidi A, Khetarpal RK, Koganezawa H (eds) Plant virus disease control. APS, St Paul, pp 277–287 29. Cassells AC, Minas G, Bailiss KW (1982) Pelargonium clear vein agent (PCVA) and Pelargonium petal streak agent (PPSA): beneficial infections of commercial Pelargonium. Sci Hortic 1:89–96 30. Lelliott RA, Stead DE (1987) Methods for the diagnosis of bacterial diseases of plants. Blackwell, Oxford 31. Schaad NW, Jones JB, Chun W (2001) Laboratory guide for identification of plant pathogenic bacteria. APS, St Louis 32. Fletcher J, Wayadande A (2002) Fastidious vascular-colonizing bacteria. Plant Health Instructor. doi:10.1094/PHI-I-2002-1218-02 33. Bove JM, Garnier M (2003) Phloem- and xylem-restricted plant pathogenic bacteria. Plant Sci 164:423–438 34. Hoffman PN, Death DE, Coates D (1981) The stability of sodium hypochlorite solutions. In: Collins CH, Allwood MC, Bloomfield SJ, Fox A (eds) Disinfectants: their use and evaluation of effectiveness. Academic, London, pp 77–83 35. Menard D, Coumans M, Gaspar TH (1985) Micropropagation du Pelargonium a partir de meristems. Meded Fac Landbouwett Rijksuniv Gent 50:327–331 36. Barnett HL, Hunter BB (1998) Illustrated genera of imperfect fungi, 4th edn. APS, St Louis 37. Cassells AC, Rafferty-McArdle SM (2012) Priming of plant defences by PGPR against fungal and bacterial plant foliar pathogens. In: Maheshwari DK (ed) Bacteria in agrobiology: stress management Springer Verlag, Berlin, pp 1–26 38. Holland MA, Polacco JC (1994) PPFMs and other covert contaminants: is there more to plant physiology than just the plant? Annu Rev Plant Physiol 45:197–209 39. Herman EB (1990) Non-axenic plant tissue culture: possibilities and opportunities. Acta Hortic 280:233–238 40. Liu L, Kloepper JW, Tuzun S (1995) Induction of systemic resistance in cucumber against bacterial angular leaf spot by plant growth-promoting rhizobacteria. Phytopathology 85:843–847 41. Garcia de Salamone IE, Hynes RK, Nelson LM (2001) Cytokinin production by plant growth promoting rhizobacteria and selected mutants. Can J Microbiol 47:404–411 42. Cassells AC, Harmey MA, Carney BF, McCarthy E, McHugh A (1988) Problems posed by cultivable endophytes in the

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establishment of axenic cultures of Pelargonium x domesticum. Acta Hortic 225:153–162 Barrett C, Cassells AC (1994) An evaluation of antibiotics for the elimination of Xanthomonas campestris pv. Pelargonii (Brown) from Pelargonium x domesticum cv. Grand Slam explants in vitro. Plant Cell Tissue Organ Cult 36:169–175 Pollack K, Barfield DG, Shields R (1983) The toxicity of antibiotics to plant tissue cultures. Plant Cell Rep 2:36–39 Walsh C (2003) Antibiotics, actions, origins, resistance. ASM, Washington, DC Falkiner FR (1988) Strategy for the selection of antibiotics for use against common bacterial pathogens and endophytes of plants. Acta Hortic 225:53–56 Cassells AC, Long RD (1980) The regeneration of virus-free plants from cucumber mosaic virus- and potato virus Y-infected tobacco explants cultured in the presence of Virazole. Z Naturforsch 35c:350–351 Cassells AC, Long RD (1982) The elimination of potato viruses X, Y, S and M in meristem and explants cultures of potato in the presence of Virazole. Potato Res 25:165–173 O’Herlihy EA, Cassells AC (2003) Influence of in vitro factors on titre and elimination of model fruit tree viruses. Plant Cell Tissue Organ Cult 72:33–42 Dijkstra J, de Jager CP (1998) Practical plant virology: protocols and exercises. Springer, Berlin Noordam D (1974) Identification of plant viruses: methods and experiments. Wageningen, Bernan Clark MF, Adams AN (1977) Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. J Gen Virol 34:475–483 Schaad NW, Frederick RD, Shaw J, Schneider WL et al (2003) Advances in molecular diagnostics in meeting crop biosecurity and phytosanitary issues. Annu Rev Phytopathol 41:305–324 Buckingham L, Flaws ML (2007) Molecular diagnostics: fundamentals, methods and clinical applications. FA Davis, Philadelphia Stead DE, Elphinstone JG, Weller S, Smith N, Hennessy J (2000) Modern methods for characterizing, identifying and detecting bacteria associated with plants. Acta Hortic 530:45–60 George AJT, Urch CE (2010) Diagnostic and therapeutic antibodies. Springer, New York Sutula CL, Gillett JM, Morrissey SM, Ramsdell DC (1986) Interpreting ELISA data and establishing the positive-negative threshold. Plant Dis 70:722–726

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75. Berg G, Eberl L, Hartmann A (2005) The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ Microbiol 7:1673–1685 76. Van der Linde PCG (2000) Certified plants from tissue culture. Acta Hortic 530:93–102

Chapter 7 Cryopreservation of Embryogenic Cell Suspensions by Encapsulation–Vitrification and Encapsulation–Dehydration Zhenfang Yin, Long Chen, Bing Zhao, Yongxing Zhu, and Qiaochun Wang Abstract Encapsulation–vitrification and encapsulation–dehydration are two newly developed techniques for cryopreservation of embryogenic cell suspensions. Here, we describe the two protocols using grapevine (Vitis) as a model plant. Cell suspensions at the exponential growth stage cultured in a cell suspension maintenance medium are encapsulated to form beads, each being about 4 mm in diameter and containing 25% cells. In the encapsulation–vitrification procedure, the beads are stepwise precultured in increasing concentrations of sucrose medium up to 0.75 M, with 1 day for each concentration. The precultured beads are treated with a loading solution for 60 min and then dehydrated with plant vitrification solution 2 at 0°C for 270 min before a direct immersion in liquid nitrogen. Following cryostorage, the beads are rapidly rewarmed at 40°C for 3 min and then unloaded with 1 M sucrose solution for 30 min. In the encapsulation–dehydration procedure, the beads are precultured in increasing concentrations of sucrose medium up to 1 M, with 1 day for each concentration, and then maintained on 1 M sucrose medium for 3 days. The precultured beads are dehydrated for 6 h under a sterile air flow, prior to rapid freezing in liquid nitrogen. The freezing and rewarming procedures are the same as used in the encapsulation–vitrification technique. The unloaded beads from encapsulation–vitrification and rewarmed beads from encapsulation–dehydration are postcultured on a recovery medium for 3 days at 25°C in the dark for survival. Surviving cells are transferred to a regrowth medium to induce cell proliferation. Embryogenic cell suspensions are reestablished by suspending the cells in a cell suspension maintenance medium maintained on a gyratory shaker at 25°C in the dark. For plant regeneration, surviving cells are transferred from the recovery medium to an embryo maturation medium and maintained at 25°C under light conditions. Embryos at the torpedo stage are cultured on a rooting medium until whole plantlet regenerates. Key words: Cell suspensions, Cryopreservation, Dehydration, Encapsulation, Somatic embryogenesis, Vitrification

1. Introduction Embryogenic cell suspensions have widely been used as an efficient system for plant clonal micropropagation and as target tissues for genetic manipulation in many transformation systems (1). However, establishment of embryogenic cell cultures is difficult (1–3). Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_7, © Springer Science+Business Media, LLC 2012

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Once established, cell cultures have to be maintained in vitro by repeated subculture. In vitro maintenance may create risks of culture loss due to contamination or human error during culture (2, 3). Moreover, the morphogenetic potential of embryogenic cultures declines or gets totally lost and genetic alterations may occur as subculture times increase (2–4). Cryopreservation has been considered as an ideal means for long-term storage of plant genetic resources, which can avoid loss of embryogenic potential and prevent occurrence of somaclonal variation, since all cell divisions and other metabolic processes of the plant materials stored in this way are arrested (5). Theoretically, plant materials can thus be stored without any changes for an indefinite period of time (5). Encapsulation–vitrification and encapsulation–dehydration are among the newly developed cryogenic methods (6–8), which allow samples to be directly immerged into liquid nitrogen, thus eliminating the usage of sophisticated and expensive programmable-controlled freezer that is required in two-step freezing method (5, 6). These two methods are receiving increasing interests and being widely used for cryopreservation of cell suspensions (2, 7). Some examples of successful cryopreservation of cell suspensions by encapsulation–vitrification and encapsulation–dehydration in recent years are documented in Table 1.

Table 1 Some examples of successful cryopreservation of cell suspensions by encapsulation–vitrification and encapsulation–dehydration techniques Plant species

Method

No. of cultivars

Survival (%)

Ref.

Arabidopsis spp.

En–dehy

1

87

(9)

A. thaliana

En–dehy

1

34

(10)

Catharanthus roseus

En–dehy

1

50

(11)

Chaetoceros muelleri

En–vitri

1

48

(12)

Gentiana cruciata

En–dehy

1

83

(13)

G. tibetica

En–dehy

1

68

(13)

Medicago sativa

En–dehy

1

25

(14)

Nitzschia closterium

En–vitri

1

74

(12)

Polygonum aviculare

En–dehy

1

Not specified

(15)

Vaccinium pahalae

En–dehy

1

30

(16)

Vitis vinifera

En–dehy En–vitri

1 4

78 46–82

(17) (18)

V. berlandieri × V. rupestris

En–vitri

1

76

(18)

V. vinifera × V. berlandieri

En–vitri

1

42

(18)

En–dehy encapsulation–dehydration, En–vitri encapsulation–vitrification

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1.1. Encapsulation– Vitrification

Encapsulation–vitrification, which is a combination of encapsulation– dehydration and vitrification procedures, is one of several newly developed techniques for cryopreservation of plant germplasm. Vitrification refers to the physical process by which a highly concentrated cryoprotective solution is supercooled at very low temperatures and eventually solidifies into a metastable glass without undergoing crystallization at a glass-transition temperature (19). Thus, vitrified cells are able to evade the danger of intracellular freezing and to survive freezing in liquid nitrogen. Encapsulation of cell suspensions, normally in 2–3% calcium-alginate beads, can protect the specimen and reduce the chemical toxicity or osmotic stress of the vitrification solution. In addition, encapsulation– vitrification is much easy to handle and can be used to simultaneously treat a large number of samples, compared with vitrification procedure alone. Encapsulation–vitrification was originally developed by Tannoury et al. (20) for cryopreservation of carnation apices (Dianthus caryophyllus L.). In this protocol, encapsulated apices were precultured for 16 h in progressively more concentrated sucrose medium, then incubated for 6 h in a vitrification solution containing ethylene glycol and sucrose, and finally frozen in liquid nitrogen. In comparison with encapsulation–dehydration, encapsulation– vitrification produced high recoveries in cryopreserved shoot tips, such as wasabi (Wasabia japonica) (21) and strawberry (Fragaria × Ananassa Duch.) (22). With embryogenic cell suspensions, Wang et al. (18) also demonstrated that encapsulation–vitrification was much more applicable to different grapevine (Vitis) species and cultivars than encapsulation–dehydration. Therefore, encapsulation–vitrification would have a great potential for much broader applications to cell suspensions (2, 3, 8).

1.2. Encapsulation– Dehydration

Encapsulation–dehydration is based on the technology developed for producing synthetic seeds, i.e., the encapsulation of explants in calcium alginate (7, 23). Encapsulated explants are then precultured with a high sucrose concentration and partially desiccated before a direct exposure to liquid nitrogen (7). Desiccation is usually performed in a laminar airflow cabinet, but more precise and reproducible dehydration conditions can be achieved by using a flow of sterile compressed air or silica gel (24). In general, water content of the beads that ensures highest regrowth following cryostorage is about 20% on a fresh weight basis, which corresponds to the amount of unfreezable water in the samples (3, 7, 24). Encapsulation of the cells allows the application of subsequent preculture with high sucrose concentrations and drastic dehydration to low moisture contents prior to freezing in liquid nitrogen, which would otherwise be highly damaging or lethal to nonencapsulated samples (7, 23, 25).

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Encapsulation–dehydration was originally developed by Dereuddre and Fabre for cryopreservation of Solanum shoot tips (26). In this protocol, encapsulated apices were precultured in progressively more concentrated sucrose medium, then dehydrated under a sterile airflow for 4 h, and finally frozen either rapidly or slowly in liquid nitrogen. Encapsulation–dehydration is a very efficient cryopreservation technique which is simple to implement and easy to manipulate throughout the freezing protocol. Encapsulation–dehydration procedure has been successfully implemented with a large number of species, including agricultural (3, 27) and horticultural (6) crops.

2. Materials 2.1. General Requirements

1. Standard tissue culture facilities. 2. Cryogenic vial (2 mL). 3. Erlenmeyer flask (250 mL). 4. Gyratory shaker. 5. Pipette (1 mL). 6. Sterile disposable pipette (25 mL). 7. Taylor-Wharton Dewar flask (beaker style wide-mouth, 20–35 L). 8. Magenta GA7 vessels. 9. Whatman paper (9 cm in diameter).

2.2. Chemicals, Plant Growth Regulators, and Media

1. Activated charcoal (AC, Sigma, C9157). 2. Calcium chloride (Sigma, C4901). 3. Casein enzymatic hydrolysate (Sigma, C7290). 4. Dimethylsulfoxide (DMSO, Sigma, D8418). 5. Ethylene glycol (Sigma, E9129). 6. Gelrite (Sigma, G1910). 7. Glycerol (Sigma, G5516). 8. Maltose (Sigma, M5885). 9. Naphthalene acetic acid (NAA, Sigma, N0640). 10. 2-naphthoxyacetic acid (NOA, Sigma, N3019). 11. Nitsch and Nitsch medium (NN (28), Duchefa, N0224). 12. Sodium alginate (Sigma, A2158). 13. Sucrose (Sigma, S7903). 14. Woody plant medium (WPM (29), Duchefa, M0220).

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2.3. Media and Solutions

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1. 0.1 M calcium chloride solution: Liquid NN medium containing 0.1 M calcium chloride, 2 M glycerol, and 0.4 M sucrose, pH 5.8. 2. Cell suspension maintenance medium: Liquid NN medium supplemented with 18 g/L maltose, 1 g/L casein enzymatic hydrolysate, 4.6 g/L glycerol, and 1 mg/L NOA, pH 5.8. 3. Embryo maturation medium: Solid NN medium supplemented with 18 g/L maltose, 1 g/L casein enzymatic hydrolysate, 4.6 g/L glycerol, and 2.6 g/L gelrite, pH 5.8. 4. Loading solution: Liquid NN containing 2 M glycerol and 0.4 M sucrose, pH 5.8. 5. Plant vitrification solution 2 (PVS2) (30): 0.4 M sucrose, 30% (w/v) glycerol, 15% (w/v) DMSO, and 15% (w/v) ethylene glycol made up in liquid NN medium, pH 5.8. 6. Plant regeneration medium: Solid NN medium supplemented with 18 g/L maltose, 1 g/L casein enzymatic hydrolysate, 4.6 g/L glycerol, and 2.6 g/L gelrite, pH 5.8. 7. Preculture medium: Cell suspension maintenance medium supplemented with 0.25, 0.5, 0.75, and 1.0 M sucrose, respectively, pH 5.8. 8. Recovery medium: Cell suspension maintenance medium containing 2.5 g/L AC and solidified with 2.6 g/L gelrite, pH 5.8. 9. Regrowth medium: Cell suspension maintenance medium solidified with 2.6 g/L gelrite, pH 5.8. 10. Rooting medium: Solid WPM containing 30 g/L sucrose, 1 mg/L NAA, 2.5 g/L AC, and 2.6 g/L gelrite, pH 5.8. 11. Sodium alginate solution: 0.4 M sucrose, 2 M glycerol, and 2.5% (w/v) sodium alginate made up in liquid NN medium, pH 5.8. 12. Unloading medium: Liquid NN medium containing 1 M sucrose, pH 5.8.

3. Methods As with any method, optimal treatment parameters at each step during the whole procedure may vary greatly with different plant species and even cultivars. In this section, we make every effort to illustrate two protocols: encapsulation–vitrification and encapsulation–dehydration using grapevine (Vitis) as an example. The encapsulation–vitrification protocol consists of (a) maintenance of embryogenic cell suspensions; (b) encapsulation–vitrification; (c) freezing and rewarming; (d) unloading; and (e) survival, regrowth, and plant regeneration, while the main steps involved in encapsulation–dehydration procedure include (a) maintenance

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Fig. 1. A flowchart of cryopreservation of embryogenic cell suspensions by encapsulation–vitrification.

of embryogenic cell suspensions; (b) encapsulation–dehydration; (c) freezing and rewarming; and (d) survival, regrowth, and plant regeneration. Flowcharts of the two protocols are illustrated in Figs. 1 and 2, respectively. To maintain sterility of embryogenic cell suspensions, all appropriate manipulations should be carried out in a laminar airflow cabinet using aseptic techniques and sterile materials. 3.1. Encapsulation– Vitrification 3.1.1. Maintenance of Embryogenic Cell Suspensions

1. Calli (1 g) are transferred to a 250-mL Erlenmeyer flask containing 50 mL of cell suspension maintenance medium to establish cell suspensions. 2. The cell suspensions are incubated at 25°C in darkness on a gyratory shaker at 90 rpm. 3. Subculture is weekly carried out by transfer of cell suspensions to fresh cell suspension maintenance medium.

3.1.2. Encapsulation– Vitrification

1. Three days after subculture (see Note 1), embryogenic cell suspensions are collected by using a sterile disposable 25-mL pipette to remove the entire liquid medium from the 250-mL Erlenmeyer flask. In order to avoid loss of cells while the liquid medium is emptied, the mouth of the pipette is pressed against the bottom of the Erlenmeyer so that the cells do not penetrate into the pipette.

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Fig. 2. A flowchart of cryopreservation of embryogenic cell suspensions by encapsulation–dehydration.

2. The cells are transferred to sodium alginate solution at a ratio of 1 g cells to 3 mL solution (see Note 2) and mixed well. 3. The mixture is dripped with a sterile pipette (1 mL) into 0.1 M calcium chloride solution and left for 20 min to form beads, each being about 4 mm in diameter and containing 25% cells (see Note 2). 4. The beads are precultured stepwise on the preculture medium enriched with increasing sucrose concentrations of 0.25, 0.5, and 0.75 M for 3 days, with 1 day for each step (see Note 3). The preculture conditions are the same as for the maintenance of embryogenic cell suspensions. 5. The precultured beads are rapidly surface dried by blotting onto sterile Whatman paper for a few seconds, then transferred to the loading solution, and incubated for 60 min in a laminar airflow cabinet (see Note 4). 6. The beads are rapidly surface dried by blotting onto sterile Whatman paper for a few seconds, then transferred to PVS2 cooled on ice, and incubated at 0°C for 270 min (see Note 5).

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3.1.3. Freezing and Rewarming

1. The vitrified beads are rapidly surface dried by blotting on sterile Whatman paper for a few seconds. Next, ten beads are transferred into a 2-mL cryogenic vial and directly immersed in a Taylor-Wharton Dewar flask containing liquid nitrogen for 1 h. 2. Cryogenic vials containing frozen cells are rapidly removed from liquid nitrogen and immediately rewarmed at 40°C in a water bath for 3 min.

3.1.4. Unloading

1. Rewarmed beads are placed in the unloading medium for 30 min (see Note 6).

3.1.5. Survival, Regrowth, and Plant Regeneration

1. The beads are postcultured at 25°C in the dark for 3 days in 9-cm Petri dishes (ten beads/dish) containing 30 mL recovery medium for survival (see Note 7). 2. For regrowth, the beads are transferred from the recovery medium to 9-cm Petri dishes (ten beads/dish) containing 30 mL regrowth medium and placed at 25°C in the dark for 4 weeks (see Note 8). Embryogenic cell suspensions are reestablished by suspending the beads in a 250-mL Erlenmeyer flask containing 50 mL of cell suspension maintenance medium. The cultures are placed on a gyratory shaker (90 rpm) at 25°C in the dark. Subculture is carried out every week. 3. For plant regeneration, the beads are transferred from the recovery medium to 9-cm Petri dish (ten beads/dish) containing 30 mL plant regeneration medium. The cultures are maintained at 25°C under a 16 h photoperiod with a light intensity of 45 μmol/s1/m2 provided by cool white fluorescent tubes. Four weeks later, single embryos at the torpedo stage are transferred to Magenta GA7 vessels containing 50 mL rooting medium. The culture conditions are the same as for embryo maturation. Subculture is done every 4 weeks until a whole plantlet with a profuse root system is developed.

3.2. Encapsulation– Dehydration

This step is exactly the same as described above in the encapsulation–vitrification procedure (18).

3.2.1. Maintenance of Embryogenic Cell Suspensions 3.2.2. Encapsulation– Dehydration

1. Collection of embryogenic cell suspensions and encapsulation are the same as described above in encapsulation–vitrification (18). 2. Following encapsulation, the beads are stepwise precultured on the preculture medium enriched with increasing sucrose concentrations of 0.25, 0.5, 0.75, and 1.0 M for 4 days, with 1 day for each step, and then maintained on 1 M sucrose for 3 days (see Note 3). The preculture conditions are the same as for the maintenance of embryogenic cell suspensions.

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3. The precultured beads are rapidly surface dried by blotting with cellulose tissue for a few seconds, placed on sterilized filter paper in 9-cm Petri dish, and dehydrated by air in a laminar flow chamber at room temperature for about 6 h, at which water content in beads is reduced to about 20.6% on a fresh weight basis (see Note 9). 3.2.3. Freezing and Rewarming

1. Following dehydration, ten precultured beads are transferred into a 10-mL cryogenic vials and immersed directly in a TaylorWharton Dewar flask containing liquid nitrogen for 1 h. 2. Cryogenic vials containing frozen cells are rapidly removed from liquid nitrogen and immediately rewarmed at 40°C in a water bath for 3 min.

3.2.4. Survival, Regrowth, and Plant Regeneration

Steps involved in survival, regrowth, and plant regeneration are exactly the same as described above in the encapsulation–vitrification procedure (18).

4. Notes 1. Growth phase at which cells are harvested at the onset of the procedure is an important factor for cryopreservation (31). Cells at the exponential growth stage are more tolerant to freezing than those either at the lag or stationary stage because they have small volume and vacuoles, and contain relatively little water. The growth pattern of cell suspensions differs with different plant species. For several Vitis species and cultivars, the exponential growth stage is reached 3 days after each subculture (17, 18). 2. Cell density in the beads influences significantly the regrowth and embryo formation of crypreserved cell suspensions. In general, 25–50% cell density was used in encapsulated beads (11, 16–18). Regrowth of cryopresereved cells of Catharanthus was found faster in the beads containing 50% than 25% cells (11), while efficiency of embryo formation in Vitis was much higher in beads containing 25% cells (17, 18). 3. Preculture is required to induce resistance of cell suspensions to dehydration and subsequent freezing in liquid nitrogen. Sucrose is the most often used sugar for induction of such tolerance at this step (5), although other sugars, such as glucose (32), glycerol (33), maltose (34), manitol (35), and sorbitol (34, 36), were used. Sugar concentration used in the preculture medium ranges from 0.3 to 1.0 M for periods varying between 1 h (34) and 9 days (11). Progressive increase in sucrose concentration enables to avoid the deleterious effects

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of direct exposure to high sucrose concentrations (37). Preculture with high sugar concentrations (up to 0.75 or 1.0 M) has been shown to increase the viability of cryopreserved cell suspensions of Catharanthus roseus (11), Papaver somniferum (34), Vaccinium pahalae (16), Medicago sative (14), Asparagus officinalis (38), and Vitis (17, 18). 4. In vitrification-based cryopreservation procedures, cells have to be dehydrated by exposure to a highly concentrated solution, such as PVS2, prior to immersion in liquid nitrogen. However, direct exposure of cells to PVS2 without osmoprotection causes harmful effects on cells because of osmotic stress or chemical toxicity (39), which has been described as a major limitation in determining the success of cryopreservation of cells by vitrification (40). This major limitation can be overcome by the loading treatment (39, 40). In this treatment, cells are placed at room temperature in a solution containing cryoprotective substances, such as sucrose, glycerol, and ethylene glycol, for a short period varying between 10 (40, 41) and 60 min (18), depending on plant species. The most often used loading solution is composed of a basic medium containing 2 M glycerol and 0.4 M sucrose (18, 40, 41). 5. Two plant vitrification solutions are most frequently employed: one described by Langis et al. (42), which comprises 40% (w/v) ethylene glycol, 15% sorbitol, and 6% bovine serum albumin, and the other (PVS2) described by Sakai et al. (30), which consists of 30% (w/v) glycerol, 15% (w/v) ethylene glycol, and 15% (w/v) DMSO. We applied both vitrification solutions to Vitis cell suspensions with much better results obtained with PVS2. Overexposure to the vitrification solution can cause chemical toxicity and excess osmotic stress (43), eventually leading to reduced survival of cryopreserved cells. Dehydration can be performed either at 0°C or room temperature. The optimal time of exposure to the vitrification solution varies with plant species, and depending on the temperature during exposure, it ranges from 20 (40) to 270 min (18). Dehydration at 0°C takes longer time, but usually yields a higher survival of cryopreserved cells (18, 40), mainly through elimination or reduction in the chemical toxicity or osmotic stress of vitrification solutions to plant cells (44). 6. Unloading is designed to dilute the vitrification solutions and remove cryoprotectants from cryopreserved cell suspensions (45). Because of the extremely high concentrations of the vitrification solutions, unloading is usually performed either by a one-step dilution in a high sugar concentration solution up to 1.2 M (40) or by a stepwise dilution in decreasing sugar concentrations (14) in order to reduce the osmotic shock. With Vitis cell suspensions, the best results were achieved using 1 M sucrose solution for 30 min (18).

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7. In many cases, recovery of cryopreserved cell suspensions was largely improved when postcultured for a few days on a solid medium before being transferred to liquid medium (18, 46). Addition of activated charcoal to the recovery medium was also found beneficial to the survival of cryopreserved cell suspensions (5, 17, 18). The beneficial effect of activated charcoal on survival was probably achieved through reduced necrogenesis (46) and adsorption of toxic substances produced by frostdamaged cells (47). 8. Regrowth of cryopreserved cell suspensions generally starts after a lag period that usually lasts from 3 (40) to 10 days (48) and reaches the same growth pattern as that of noncryopreserved cell suspensions after two to three times of subculture (17, 18). 9. Two desiccation methods can be employed: dehydration under the air current of a laminar flow cabinet or dehydration in sealed containers with dry silica gel. In general, the bead water content that ensures the highest regrowth following cryopreservation is around 20% on a fresh weight basis (3, 7, 24), which corresponds to the amount of unfreezable water in the samples. At such water contents, only glass transitions are recorded by differential scanning calorimetry when samples are plunged in LN (49). This value may vary depending on the species and the type of samples. References 1. Raemakers K, Jacobsen E, Visser R (1999) Proliferative somatic embryogenesis in woody species. In: Jain SM, Gupta PK, Newton RJ (eds) Somatic embryogenesis in woody plants, vol 4. Kluwer, Dordrecht, pp 29–59 2. Lambardi M, Ozudogru EA, Benelli C (2008) Cryopreservation of embryogenic cultures. In: Reed BM (ed) Plant cryopreservation: a practical guide. Springer, Berlin, pp 177–210 3. Feng CH, Yin ZF, Ma YL et al (2011) Cryopreservation of sweetpotato and its pathogen elimination by cryotherapy. Biotechnol Adv 29:84–93 4. Harding K (1996) Approaches to assess the genetic stability of plants recovered from in vitro culture. In: Normah MN, Narimah MK, Clyde MMJ (eds) Techniques in in vitro conservation. University Kebangsaan, Malaysia, pp 135–168 5. Engelmann F (1997) In vitro conservation methods. In: Callow JA, Ford-Lloyd BV, Newbury HJ (eds) Biotechnology and plant genetic resources. CAB, Oxford, pp 119–161 6. Wang QC, Perl A (2006) Cryopreservation in floricultural crops. In: Teixeira da Silva JA (ed)

Floricultural, ornamental and plant biotechnology: advances and topics. Global Science, London, pp 523–539 7. Engelmann F, Gonzalez-Arnao M-T, Wu YJ et al (2008) The development of encapsulation dehydration. In: Reed BM (ed) Plant cryopreservation: a practical guide. Springer, Berlin, pp 59–75 8. Sakai A, Hirai D, Niino T (2008) Development of PVS-based vitrification and encapsulationvitrification protocols. In: Reed BM (ed) Plant cryopreservation: a practical guide. Springer, Berlin, pp 33–57 9. Ogawa Y, Suzuki H, Sakurai N (2008) Cryoperservation and metabolic profiling analysis of Arabidopsis T87 suspension-cultured cells. Cryo Letters 29:427–436 10. Bachiri Y, Bajon C, Sauvanet A et al (2000) Effect of osmotic stress on tolerance of air-drying and cryopreservation of Arabidopsis thaliana suspension cells. Protoplasma 214:227–243 11. Bachiri Y, Gazeau C, Hansz J et al (1995) Successful cryopreservation of suspension cells by encapsulation-dehydration. Plant Cell Tissue Organ Cult 43:241–248

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12. Zhang ED, Zhang LJ, Wang B et al (2009) Cryopreservation of marine diatom algae by encapsulation-vitrification. Cryo Letters 30: 224–231 13. Mikula A, Olas M, Sliwinska E et al (2008) Cryopreservation by encapsulation of Gentiana spp. cell suspension maintains regrowth, embryogenic competence and DNA content. Cryo Letters 29:409–418 14. Shibli RA, Haagenson DM, Cunningham SM et al (2001) Cryopreservation of alfalfa (Medicago sativa L.) cells by encapsulationdehydration. Plant Cell Rep 20:445–450 15. Swan TW, Deakin EA, Hunjan G et al (1998) Cryopreservation of cell suspensions of Polygonum aviculare using traditional controlled rate freezing and encapsulation/dehydration protocols, a comparison of post-thaw cell recovery. Cryo Letters 19:237–248 16. Shibli RA, Smith MAL, Shatnawi MA (1999) Pigment recovery from encapsulated-dehydrated Vaccinium pahalae (ohelo) cryopreserved cells. Plant Cell Tissue Organ Cult 55:119–123 17. Wang QC, Gafny R, Sahar et al (2002) Cryopreservation of grapevine (Vitis vinifera L.) embryogenic cell suspensions by encapsulationdehydration and subsequent plant regeneration. Plant Sci 162:551–558 18. Wang QC, Mawassi M, Sahar N et al (2004) Cryopreservation of grapevine (Vitis spp.) embryogenic cell suspensions by encapsulationvitrification. Plant Cell Tissue Organ Cult 77:267–275 19. Fahy GM, MacFarlande DR, Angell CA et al (1984) Vitrification as an approach to cryopreservation. Cryobiology 21:407–426 20. Tannoury M, Ralambosoa J, Kaminski M et al (1991) Cryopreservation by vitrification of coated shoot tips of carnation (Dianthus caryophyllus L.) cultured in vitro. Comptes Rendus de l’Acad des Sci Paris Serie III 313:633–638 21. Matsumoto T, Sakai A, Yamada K (1994) Cryopreservation of in vitro-grown apical meristems of wasabi (Wasabia japonica) by vitrification and subsequent high plant regeneration. Plant Cell Rep 13:442–446 22. Hirai D, Shirai K, Shirai S et al (1998) Cryopreservation of in vitro-grown meristems of strawberry (Fragaria x Ananassa Duch.) by encapsulation-vitrification. Euphytica 101: 109–115 23. Redenbaugh K, Paasch BD, Nichol JW et al (1986) Somatic seeds: encapsulation of asexual plant embryos. Biotechnology 4:797–801 24. Gonzalez-Arnao MT, Panta A, Roca WM et al (2008) Development and large scale application of cryopreservation techniques for shoot and

somatic embryo cultures of tropical crops. Plant Cell Tissue Organ Cult 92:1–13 25. Gonzalez-Arnao MT, Engelmann F (2006) Cryopreservation of plant germplasm using the encapsulation-dehydration technique: review and case study on sugarcane. Cryo Letters 27:155–168 26. Fabre J, Dereuddre J (1990) Encapsulationdehydration: a new approach to cryopreservation of Solanum shoot tips. Cryo Letters 11:413–426 27. Wang B, Yin ZF, Feng CH et al (2008) Cryopreservation of potato shoot tips. In: Benkeblia N, Tennant P (eds) Potato I. Fruit, vegetable and cereal science and biotechnology, vol 2, special issue 1. Global Science, London, pp 46–53 28. Nitsch JP, Nitsch C (1969) Haploid plants from pollen grains. Science 163:85–87 29. Lloyd G, McCown B (1980) Commercially feasible micropropagation of mountain laurel, Kalmia latifolia, by use of shoot-tip culture. Proc Intl Plant Prop Soc 30:421–427 30. Sakai A, Kobayashi S, Oiyama I (1990) Cryopreservation of nucellar cells of navel orange (Citrus sinensis Osb. var. brasiliensis Tanaka) by vitrification. Plant Cell Rep 9:30–33 31. Reinhoud PJ, Iren FV, Kijne JK (2000) Cryopreservation of undifferentiated plant cells. In: Engelmann F, Takagi H (eds) Cryopreservation of tropical plant germplasm. JIRCAS, Japan, pp 212–216 32. Jitsuyama Y, Suzuki T, Harada T et al (1997) Ultrastructural study on mechanism of increased freezing tolerance due to extracelluar glucose in cabbage leaf cells. Cryo Letters 18:33–44 33. Touchell DH, Chiang VI, Tsai C-J (2001) Cryopreservation of embryogenic cultures of Picea mariana (black spruce) using vitrification. Plant Cell Rep 21:118–124 34. Gazeau C, Elleuch H, David A et al (1998) Cryopreservation of transformed Papaver somniferum cells. Cryo Letters 19:147–159 35. Ribeiro RCS, Jekkel Z, Mulligan BJ et al (1996) Regeneration of fertile plants from cryopreserved cell suspensions of Arabidopsis thaliana (L.) Heynh. Plant Sci 115: 115–121 36. Touchell DK, Chiang VL, Tsai C-J (2002) Cryopreservation of embryogenic cultures of Picea mariana (Black spruce) using vitrification. Plant Cell Rep 21:118–124 37. Plessis P, Leddet C, Dereuddre J (1991) Resistance to dehydration and to freezing in liquid nitrogen of alginate coated shoot tips of grapevine (Vitis vinifera L. cv. Chardonnay). Comptes Rendus de l’Acad Sci Paris Serie III 313:373–380

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38. Jitsuyama Y, Suzuki T, Harada T et al (2002) Sucrose incubation increases freezing tolerance of asparagus (Asparagus officinalis L.) embryogenic cell suspensions. Cryo Letters 23: 103–112 39. Ishikawa M, Tandon P, Suzuki M et al (1996) Cryopreservation of bromegrass (Bromus inermis Leyss) suspension cultured cells using slow prefreezing and vitrification procedures. Plant Sci 120:81–88 40. Nishizawa S, Sakai A, Amano Y et al (1993) Cryopreservation of asparagus (Asparagus officinalis L.) embryogenic suspension cells and subsequent plant regeneration by vitrification. Plant Sci 91:67–73 41. Sakai AK, Kobayashi S, Oiyama I (1991) Survival by vitrification of nucelar cells of navel orange (Citrus Sinensis var. brasiliensis Tanaka) cooled to -196°C. J Plant Physiol 137:465–470 42. Langis R, Schnabel B, Earle ED et al (1989) Cryopreservation of Brassica campestris L. suspensions by vitrification. Cryo Letters 10: 421–428 43. Rall WF (1987) Factors affecting the survival of mouse embryos cryopreserved by vitrification. Cryobiology 24:367–402

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44. Matsumoto T, Sakai A (2003) Cryopreservation of axillary shoot tips of in vitro-grown grape (Vitis) by a two-step vitrification protocol. Euphytica 131:299–304 45. Steponkus PL, Langis R, Fujikawa S (1992) Cryopreservation of plant tissue by vitrification. In: Steponkus PL (ed) Advances in low temperature biology, vol 1. JAI, London, pp 1–61 46. Dussert D, Mauro MC, Engelmann F (1992) Cryopreservation of grape embryogenic cell suspensions. 2: Influence of post-culture conditions and application to different strains. Cryo Letters 13:15–22 47. Kuriyama A, Watanabe K, Ueno S et al (1990) Effect of post-thaw treatment on the viability of cryopreserved Lavandula vera cells. Cryo Letters 11:171–178 48. Shashi G, Vasil IK (1992) Cryopreservation of immature embryos, embryogenic callus and cell suspension cultures of gramineous species. Plant Sci 83:205–215 49. Sherlock G, Block W, Benson EE (2005) Thermal analysis of the plant encapsulationdehydration cryopreservation protocol using silica gel as the desiccant. Cryo Letters 26: 45–54

Chapter 8 The Study of In Vitro Development in Plants: General Approaches and Photography Edward C. Yeung Abstract Careful examination of how explants react to experimental conditions is the first step of a successful research program. Photographing the specimen is an extremely important method that can be used to document changes of an explant throughout an experiment. This article serves to draw attention to the utility of macroscopic and microscopic examinations in the study of in vitro development, and details some useful methods in the study of the cultured explants. Key words: Digital camera, Freehand sections, Photography, Photomicrography, Staining

1. Introduction Developmental processes are complex, and are subject to many internal and external factors and influences which complicate investigation. The use of in vitro culture systems enables researchers to isolate the explants and to reduce the complexity of the experimental system to study the problem of interest. The results often provide new insights and augment in vivo studies. This approach is powerful and is well documented in the literature (1, 2). Besides theoretical interest, the study of in vitro development is also essential to plant biotechnology; the success of shoot and root regeneration and in vitro embryogenesis are the key steps towards the development of protocols in plant transformation and genetic modification. In the course of studying a developmental process, careful evaluation of responses by the explants to experimental manipulation is essential. Thorough observation and documentation of

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_8, © Springer Science+Business Media, LLC 2012

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results is the first step towards the development of a successful protocol. Some practical comments concerning the use of histology in the study of plant tissue culture systems have been presented earlier (3, 4). The purpose of this article is to focus on simple methods and approaches used to extract information from one’s system by careful macroscopic examination of specimens. The information presented in this chapter endeavors to improve the quality of research and presentation. 1.1. How to Examine a Specimen and Evaluate the Results

Every experimental system is different, with both obvious and subtle features. How are these observed? The best answer is to use an investigative approach—ask questions as you look at a specimen. While you look, be sure to consider physiology, cell biology, and biochemical changes. “Looking and thinking” provides a dynamic interpretation of changes observed.

1.1.1. Approaches and What Needs to Be Documented

The majority of experiments should initially investigate how their explant materials respond to an in vitro culture environment, and test the effectiveness of various additives such as plant growth regulators in achieving a desired outcome, such as root and shoot regeneration. At present, numerous protocols are present in the literature that can serve as guides in the design and the initial selection of culture media and growth conditions. If there is a positive response to the initial test trial, the next step is optimization. This requires systematic testing of various parameters. In order to be convincing as a useful protocol, the following information should be presented. A careful morphological description of the starting plant material used in the experiment must be clearly stated. The information such as the age of the explants, where and how the materials were excised from the starting material, and the final size of the explants used for in vitro culture should be described carefully. This information is useful for readers to assess the developmental potential of the explants used in the experiment. The culture conditions, e.g., media composition, additives, light intensity, photoperiod, etc. should be detailed. A clear indication of what has been tested such as range of growth regulator concentrations should be clearly indicated in the text, tables, and figures. This information is necessary to justify and prove that optimization of the protocol had been performed. The response of the explants to various combinations of treatments must be documented in a quantitative manner whenever possible. The data such as percentage of explants responding to a treatment, the number of regenerated structures per explant, and the normality of regenerated structures should be documented. Normality can be illustrated with photos and conversion percentage. Conversion is the best approach to describe normality of a regenerated structure. For example, the fact that a somatic embryo can

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convert into a normal seedling within a few days of transferring to a germination medium indicates the presence of functional shoot and root meristems. Not all regenerated structures have functional meristems. Simply showing a form without further testing of normal development is unacceptable as a protocol. Another indication of the utility of a protocol is the percentage of plants that can flower and set seeds. Companion photographic documentation of changes will greatly clarify the course of development over time. Proper statistical treatment of data will also add credence to the data presented (5, 6). If all the above information can be presented together with positive outcomes, the protocol is definitely a useful method for others to follow. 1.1.2. Know Your Initial Explants

It is imperative to have a good understanding of the structure and the developmental potential of explants at the time of culture. The basic morphology and anatomy must be clearly understood. In order to appreciate the changes occurring in, for example, the nodal explant system which is a common approach used in the micropropagation of a species (7), it is important to know whether existing axillary buds are present. The newly formed shoots that one sees may originate from existing axillary and accessory buds, and are therefore not newly regenerated structures. A good understanding of the explant is thus needed in order to avoid wrong inferences.

1.1.3. Asking Questions as You Look Is the Key to a Successful Observation Process

Once the cultures are set up, visual examination should be carried out regularly. The best approach to studying changes during the course of an experiment is to ask questions. This approach provides a better focus as one examines the explant; without questions in mind, we are “blind.” Using shoot regeneration as an example, one might ask where the shoot is coming from. If it is formed near explant surface in the absence of a callus, is it derived from the epidermal or subepidermal layers? If so, meristemoids may be present (8). If the shoots come from a cut surface, vascular tissues may be responsible for their formation (9). Careful observation of swellings near or at existing vascular strands can provide clues to their origin. Are the newly formed structures somatic embryos or adventitious shoot primordia? In the case of the former, one should be able to see a narrowing of the root pole suggesting the presence of a functional root tip. Also, if the structures are loosely attached to the explants, they are likely to be somatic embryos (10). Many structures can take on a “somatic embryo-like” structure although functional meristems are absent (11, 12). In a shoot regeneration system, shoot-like structures can be present and yet they may not develop into a functional shoot. In fact, shoot-like structures can simply be leaves; hence, careful observation and further studies are required to discern the true nature of the structures observed.

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Once questions begin to be formulated, the examination will be more focused. At the beginning, simply ask one question and look for the answer one at a time. Repeat the process until all potential questions have been exhausted. Remember that the answer is in front of you. Careful observation allows for new discoveries to be made. 1.2. How to Capture the Information?

Information recording is key to any experimentation. Besides written comments, photography is a powerful way to document changes that took place. Morphological changes can be subtle and sometimes difficult to describe. Photographic records are extremely useful for enhancing written descriptions. As a general rule, one should take photos as one examines a specimen. As indicated earlier, it is also important to ask questions. Try to look for the answer and capture it with a photo to complement written notes. If a different question arises, take another set of photos, even though they can be very similar. It is important to remember that we are focusing on “living” specimens, the same exact structure may be difficult to see in a repeat experiment. Photographic records are useful for future comparisons. Be sure to examine your cultures frequently in order not to miss rapid changes that might have occurred. Certain changes occur rapidly such as color changes of cells and tissues; new root initiation can occur within 12–24 h from a regenerated shoot. Developmental processes are complex. To fully understand a process, one has to be equipped with knowledge from all areas of biology. Morphological and anatomical approaches provide appreciation for some visual changes in the explant during the course of an experiment. This is an observational approach in the study of a problem. It is important to remember that describing the changes using biochemical, molecular and cellular approaches such as presenting gene sequences, gels, etc. is just a different type of “picture,” a different way of show and tell. These approaches are not better or worse than structural presentations. Instead, all these approaches complement one another to answer the problem of interest. The power of one’s observation is the key to the success of a project. This fuels your imagination and is the basis of new discoveries. This article simply serves as a reminder of how to look at the specimens. Younger investigators tend not to pay too much attention to their culture system and fail to recognize the power of simple observation. A careful, observational, investigative approach can yield valuable results and create additional hypotheses for further testing of ideas. This chapter details protocols that are useful in the study of macroscopic changes of the explants during the course of in vitro culture.

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2. Materials 2.1. Equipment for Stereomicroscopic Observation

1. A good quality stereomicroscope preferable with a trinocular head so that a camera can be attached (see Note 1).

2.2. Dissecting Tools (See Note 3)

1. Fine forceps.

2. Lighting attachments and accessories are needed to provide the necessary light intensity for image capture (see Note 2). Ring light that attaches directly to the lens of the stereomicroscope and gooseneck fiber optics that directs light to specimens are commonly available. The new “mini-Light” from Electron Microscopy Sciences offers high light intensity with a small footprint that fits into most locations.

2. Dissecting knives. 3. Dissecting needles.

2.3. Freehand Sections

1. Double edge razor blades. 2. Supplies: small paint brush, test tubes, slides and cover glasses, Petri dishes, absorbing papers, disposable pipettes.

2.4. Staining and Mounting Solutions

1. Toluidine blue O (TBO) stain: Dissolve 0.1 g of TBO in 100 mL of 0.1 M benzoate buffer, pH 4.4 (benzoic acid 0.25 g, sodium benzoate 0.29 g, water 200 mL). This buffer is recommended for histochemical purposes. If benzoate buffer is not available, for general use, laboratory water can be used as the solvent for TBO. 2. Phloroglucinol–HCl stain: There are various recipes to make up the staining solution but commonly it is prepared as a saturated aqueous solution of phloroglucinol in 20% hydrochloric acid. The hydrochloric acid used is about 2 N. Be sure to handle the solution with care. Wear gloves. Prepare this solution in the fume hood. First dissolve phloroglucinol (about 2.0 g) in 80 mL of water and then add 20 mL of concentrated HCl (12 N) to it. 3. IKI stain: The solution is prepared by first dissolving 2 g of KI in 100 mL of water, and adding 0.2 g of iodine into the KI solution. Prepare this solution ahead of time, as iodine takes some time to dissolve. Store the solution in a dark glass bottle and cap tightly. Exposure to light and air degrades the solution’s usefulness. Iodine sublimates at room temperature. It is preferable to prepare the solution in a fume hood. The stain, once prepared, can be kept for several months or longer, as long as the bottle is tightly capped. 4. Mounting solutions: water; a 30% glycerol solution.

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2.5. Camera and Accessories

1. Digital cameras. Specialized digital cameras for photomicrography are available from major microscope vendors. Selection of a model is based on one’s own need and budget (see Note 4). 2. Black agar plates. Charcoal powder about 4% is added to a hot 1.5–2% agar solution before solidification (see Note 5). 3. Other accessories: small camera tripods, hair dryer and ruler, color cardboards for background contrast.

3. Methods 3.1. General Photography of Large Explants

1. Large explants such as plantlets from in vitro cultures can be photographed using standard digital cameras. At present, quality digital cameras are commercially available, and their price has been reduced in recent years. The macro-function enables the photography of large explants. 2. Arrange the objects such as culture boxes, Petri plates, plantlets, etc. against an even background. Cardboard and cloths can be used. 3. Label each object and be sure that the writing is legible. 4. A scale such as a ruler should be photographed together with the object. 5. Arrange the lighting equipment to avoid obvious shadow formation (see Note 6). 6. After photographing the object, be sure to look at the digital files to ensure the images are sharp showing the desired features. Otherwise retake the photos at once (see Note 7).

3.2. Photography Through a Stereomicroscope

For a detailed examination of the object, careful study using a stereomicroscope is preferred. The “zoom” feature easily allows for the change of magnification. The image can be captured using a digital camera directly attached to the stereomicroscope. Before use, one should be familiar with one’s own stereomicroscope in order to understand its capability and limitations. For a more detailed theoretical and practical treatment of this topic, see references such as ref. (13). 1. Explants can be examined without removal from the culture vessels. One can follow the developmental changes of the same explants through the course of the experiment. Photos of the specimens can be taken directly through the Petri plates or culture vessel. Condensation often occurs on the lid of a Petri plate impeding observation. It is possible to remove the condensation by using a hair dryer to evaporate the condensate from the surface of the Petri dish or culture vessel.

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2. For better close up observation, especially for smaller specimens, a representative explant can be removed from the culture vessel and placed on a black agar plate. The specimen can be examined from different angles by rotating the specimen on top of the agar plate with the help of a fine forceps. Detail surface features can be studied by using the zoom function of the stereomicroscope. The black agar plate provides a better contrast for the specimen (see Note 8). 3. A small scale bar should be placed close to the specimen to provide information about the size of the specimen. A scale bar can be created by simply photocopy of a ruler, cut off a centimeter portion of the image and place next to the specimen. 4. Proper lighting is important as it provides the proper light intensity as well as the shadowing effects highlighting the structures of interest. Ring light provides an even illumination over the entire specimen when examining the specimen using a stereomicroscope. The positioning of the gooseneck arms and or any other lights can create the shadow and provides better contrast of the specimen. Try different positions by moving the arm or other light source to obtain the best desirable image that show case the feature of interest (see Note 9). 3.3. Photomicrography of Liquid Suspension Cells and Freehand Sections

For more detailed studies of cell, small cell aggregates, and hand sections of explants, a compound light microscope is preferred, as it has a better resolving power than a stereomicroscope. 1. Dispense a small amount of liquid suspension cells or freehand sections on a slide. The cells and sections can be stained previously to improve the contrast (see Subheading 3.5). 2. Quickly place a cover glass over it with just enough liquid surrounding the cells or sections. It is imperative that no liquid should be overflowing the slide. The extra liquid can corrode the microscope stage and condenser. 3. Unstained specimens can be examined using phase contrast or interference contrast optics, if such components are present. 4. Capture the image with existing digital camera equipment.

3.4. Simple Histological and Histochemical Staining of Specimens

Certain explants such as calluses may have little color; hence, little contrast to show surface features. One way to increase the contrast of a specimen is through staining. Staining, in addition to enhancing the contrast may also provide some additional information concerning the wall features and cellular details. Thus, one can gain additional insights into the experimental system. A number of staining protocols are available in the literature that can be used to stain explants and suspension culture cells directly without the need of elaborate embedding and sectioning. For large explants that can be handled by “hand,” freehand sections (see Subheading 3.5) can be carried out prior to staining and examination. The toluidine

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blue O, phloroglucinol–HCl and IKI procedures are detailed in this section. For additional staining recipes, consult additional references (14, 15). 3.4.1. Toluidine Blue O Staining for General Histology and Histochemistry (16, 17)

TBO has the advantage of being a polychromatic dye, i.e., it reacts with different chemical components of cells differently and results in a multicolored specimen (16). The colors generated can provide information on the nature of the cell and its walls. TBO is a cationic dye that binds to negatively charged groups. An aqueous solution of this dye is blue, but different colors are generated when the dye binds with different anionic groups in the cell. For example, a pinkish purple color will appear when the dye reacts with carboxylated polysaccharides such as pectic acid; green, greenish blue or bright blue with polyphenolic substances such as lignin and tannins; and purplish or greenish blue with nucleic acids (for details, see ref. 16). General expected results are as follows: pectin, red or reddish purple; lignin, blue; other phenolic compounds, green to blue-green; thin-walled parenchyma, reddish purple; lignified elements such as tracheary elements and sclerenchyma, green to blue-green; sieve tubes and companion cells, purple; middle lamella, red to reddish purple; callose and starch, unstained (16). 1. Transfer the suspension culture to a small container such as a small tube. Remove excess culture medium using a disposable pipette with a fine tip. Apply the TBO stain to the cells and stains for 1 min. Gently remove the stain and wash the cells two times with water. Transfer the cells directly onto a clean slide, cover with a cover glass and examined with a light microscope. 2. For freehand sections, apply the TBO stain directly to the sections for 1 min. Gently remove the stain by using a piece of filter paper. Wash the sections by flooding them with water followed by its removal. Repeat until there is no excess stain around the sections. Add a drop of clean water over the material and apply a cover glass. The slide is ready for examination (see Note 10). 3. The images can be captured using a digital camera attached to the microscope.

3.4.2. Phloroglucinol–HCl Test for Lignin (18, 19)

Lignin is a common constituent in the secondary wall of plant cells, e.g., the walls of xylem elements and sclerenchyma tissue. The cinnamaldehyde end groups of lignin appear to react with phloroglucinol–HCl to give a red-violet color (18, 19). Although the reaction is not very sensitive, because of the ease of staining, this procedure is still often used as one of the tests for the presence of lignin in plant cell wall. General expected results: Lignified walls become red. 1. Since the phloroglucinol stain has a high concentration of hydrochloric acid, suspension cells, cell clusters, and hand

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sections are placed in a small Petri dish and stained with the phloroglucinol–HCl stain for 2 or more minutes. If lignified elements are present, the specimen will turn red in a few minutes. 2. Use a wet brush to transfer the cells or sections onto a clean slide, add a drop of water or a drop of 30% glycerol solution to the section. Be sure to place a cover glass over the cells or tissues before examination. Examine the specimen at once. The color fades gradually. 3. Be careful when handling the stain. Be sure that the stain does not get in contact with any part of the objective and microscope stage as the stain is highly corrosive. Wash the brush with running tap water to remove the acid. 3.4.3. Starch: Iodine– Potassium Iodide Test (18, 19)

The iodine–potassium iodide (IKI) stain is specific for starch. Apparently, the basis of the reaction is the accumulation of iodine in the center of the helical starch molecule. The length of the starch molecule determines the color of the reaction—the shorter the molecule, the more red the color; the longer the molecule, the more blue the color. General expected results: Starches will give a blueblack color in a few minutes. Newly formed starch may appear red-purple. 1. Transfer materials Subheading 3.4.1.

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2. Place a drop of IKI solution directly on the specimen. Wait for a few minutes and apply a cover glass and examine the specimen with a microscope. The specimen can be examined without the removal of excess IKI solution from the sample. 3.5. Freehand Sections

Most plant parts are too thick to be mounted intact and viewed with a microscope. In order to study the structural organization of the plant material, sections have to be made so that enough light can be transmitted through the specimen to resolve cell structures under the microscope. A freehand section is the simplest method of preparing specimens for microscopic viewing. Chemical fixation of materials is generally not required for temporary preparations. This method allows one to examine the specimen in a few minutes. For in vitro cultures, large explants can be sectioned by hand. The sectioning of smaller explants is possible but requires some practice. Many additional freehand sectioning methods are available in the literature; please consult references (14, 15, 17, 20). A detailed pictorial presentation of hand sectioning procedure can be found in (17). Figure 1a represents a soybean cotyledon explant with nodules developing from the cut surface. Corresponding hand section of the cotyledon explant shows the organization of the nodule with dense cytoplasmic cells (Fig. 1b). Histochemical staining

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Fig. 1. (a) Soybean cotyledon explants showing nodule (N) formation near the cut surface. Scale bar = 1 mm. (b) A hand section through a developing nodule showing the presence of dense cytoplasmic cells within the nodule. Scale bar = 25 μm. (c) Histochemical staining for starch using the IKI solution reveals the presence of starch granules (arrow) in cells surrounding the nodules (N). Scale bar = 25 μm.

with the IKI solution reveals the presence of starch grains in cells surrounding the nodular structure (Fig. 1c). 1. Obtain a new double edge razor blade. To minimize the risk of cutting oneself, cover one edge of the razor blade with masking tape. Rinse the blade with warm tap water to remove traces of grease from the surface of the blade if necessary (see Note 10).

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2. Hold the plant material firmly. The material should be held against the side of the first finger of the left hand (or right hand) by means of the thumb. The first finger should be kept as straight as possible, while the thumb is kept well below the surface of the material out of the way of the razor edge (17, 20). Relax! It is not that easy to cut your own finger. 3. Flood the razor with water. This will reduce the friction during cutting as sections can float onto the surface of the blade. Take the razor blade in the right hand (or left hand) and place it on the first finger of the left hand (or right hand), more or less at a right angle to the specimen (17, 20). 4. Draw the razor across the top of the material in such a way as to give the material a drawing cut (about 45° in the horizontal direction). This results in less friction as the razor blade passes through the specimen. Cut several sections at a time. The sections will certainly vary in thickness. However, there will be usable ones among the “thick” sections! 5. Transfer the sections to water, always using a brush, not a forceps or needle. 6. Select and transfer the thinnest sections (the more transparent ones) onto a glass slide and stain (see Subheading 3.2). 3.6. Digital Camera and Photomicrography

The process of photography changes dramatically with the development of digital cameras. For better quality camera, the CCD (charge coupled device) type cameras are preferred as they provide better quality images. The improvement of the CMOS (complementary metal oxide semiconductor) type cameras in recent years also makes them suitable for general photomicrography; especially, this type of camera is slightly less expensive. 1. Set up the digital camera according to manufacturer specification. 2. Be sure to understand the various features of one’s own stereomicroscope or the compound microscope in order to take full advantage of the equipment at hand. 3. Depending on how the camera is attached to the microscope, different “mounts” alter the magnification ratio of the specimen. The exact magnification can only be determined by taking a set of images of a ruler that correspond to the setting of the stereomicroscope or a fine calibrated scale for the compound microscope. These magnification calibrations are not interchangeable between scopes. 4. Capture images with specific questions in mind. 5. Examine the images and make sure they are of good/excellent quality; if not, retake the photos at once. 6. Copy images to CD or DVD format for safe keeping.

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4. Notes 1. For small explants and for a closer look at surface features, a stereomicroscope set up is preferred. Simple photomacrography requires a stereomicroscope, a light source and a digital camera. The images captured need to be transferred to a computer, and can be further manipulated with improved contrast and sharpness using appropriate software such as the Adobe Photoshop. A good quality printer is needed for printing the final composition. Depending on one’s budget, instruments with different price ranges can be found. There are many manufacturers of these instruments. Additional information can be acquired through local suppliers or the World Wide Web. The magnification power and the quality of the objective lens determine the price of a stereomicroscope. The presence of a transmitted light base is a useful feature, but will add to its cost. 2. Proper illumination of the object is essential to quality photography. A full range of devices can be found on the Electron Microscopy Sciences Web site (http://www.emsdiasum.com) for reference. 3. Dissecting tools. In order to study the specimen thoroughly, careful dissection is required. It is imperative that good quality dissecting tools are used such as fine forceps, microdissection knives and pins (see companies such as Fine Science Tools, http://www.finescience.ca). This avoids unnecessary physical damage to the explants during manipulation. 4. Digital cameras are now standard equipment and can be placed in the same light path as the microscope, using a trinocular head piece or by attaching the camera to one of the eye pieces. Again, there is a wide range of prices. The Web site from the Martin Microscope Company (http://www.martinmicroscope. com) provides useful information showing the different types of cameras available. If possible, test the camera with your stereomicroscope system before purchasing it to ensure compatibility. Software is usually purchased or included with the camera. It is important that the software be compatible with the computer system. 5. Keep plates in a refrigerator. Excess water condensation can be removed using absorbent paper or a paper towel before use. 6. Be sure not to allow the specimen to dry up during examination. The chances of this are augmented by the fact that the light source can generate quite a bit of heat. 7. The photographed specimens can be stored temporary in a refrigerator for short time (about 24 h) if rephotographing is contemplated.

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8. One way to minimize sample desiccation is to examine the explants on an agar plate. Agar is moist, so the specimen will not easily dry out during the course of photography. Agar plate can also serve as background support for the specimen during photography. Large specimens are difficult to focus at high magnifications because the depth of field of a stereomicroscope is limited. Because agar is soft, one can orientate the specimen without damaging it and easily position the feature of interest on the surface of the agar and submerge the remaining portion of the specimen. This way, the feature of attention is in focus. 9. If more light is required, reflectors can be created using aluminum foil near the specimen. Excess moisture around the specimen can cause bright reflections. It can be easily removed by small filter paper wedges. 10. Since water can evaporate from the slide over time, a 30% glycerol solution can be used instead of water. The sections will not dry out as fast as those in water. Add only a small drop of mounting medium. Excess mounting medium around the cover glass should be removed by gently touching the edge of the cover glass with a filter paper. Be sure there is no mounting fluid on the surface of the cover glass. Be sure to place a cover glass over your preparation. Use only one cover glass!

Acknowledgments I am grateful to the Natural Sciences and Engineering Research Council of Canada for the continuous funding of my research program. References 1. Wetmore RH, Wardlaw CW (1951) Experimental morphogenesis in vascular plants. Annu Rev Plant Physiol 2:269–292 2. Steeves TA, Sussex IM (1989) Patterns in plant development. Cambridge University Press, Cambridge 3. Yeung EC (1999) The use of histology in the study of plant tissue culture systems – some practical comments. In Vitro Cell Dev Biol Plant 35:137–143 4. Yeung EC, Sexena PK (2005) Histological techniques. In: Jain SM, Gupta PK (eds) Protocol for somatic embryogenesis in woody plants. Springer, Dordrecht, pp 517–537 5. Campton ME, Mize CW (1999) Statistical considerations for in vitro research: I – birth of

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an idea to collecting data. In Vitro Cell Dev Biol Plant 35:115–121 Mize CW, Koehler KJ, Compton ME (1999) Statistical considerations for in vitro research: II – data to presentation. In Vitro Cell Dev Biol Plant 35:122–126 Wong CK, Yeung EC, Wong HYS (1992) Multiple shoot formation from mature cotyledonary node of the bean. Phaseolus coccineus L. I. In vitro culture technique. Chin Agron J 2:155–167 Yeung EC, Aitken J, Biondi S, Thorpe TA (1981) Shoot histogenesis in cotyledon explants of radiata pine. Bot Gaz 142:494–501 Ogita S, Yeung EC, Sasamota H (2004) Histological analysis in shoot organogenesis

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E.C. Yeung from hypocotyls explants of Kandelia candel (Rhizophoraceae). J Plant Res 117:457–464 Bassuner BM, Lam R, Lukowitz W, Yeung EC (2007) Auxin and root initiation in somatic embryos of Arabidopsis. Plant Cell Rep 26:1–11 Nickle TC, Yeung EC (1993) Failure to establish a functional shoot meristem may be a cause of conversion failure in somatic embryos of Daucus carota (Apiaceae). Am J Bot 80: 1284–1291 Yeung EC, Stasolla C (2001) Somatic embryogenesis – apical meristems and embryo conversion. Korean J Plant Tissue Cult 27:299–307 Thomson DJ, Bradbury S (1987) An introduction to photomicrography. Oxford University Press, New York O’Brien TP, McCully ME (1981) The study of plant structure: principles and selected methods. Termarcarphi, Melbourne

15. Ruzin SE (1999) Plant microtechnique and microscopy. Oxford University Press, New York 16. O’Brien TP, Feder N, McCully ME (1964) Polychromatic staining of plant cell walls by toluidine blue O. Protoplasma 59:368–373 17. Peterson RL, Peterson CA, Melville LH (2008) Teaching plant anatomy. NRC, Canada 18. Jensen WA (1962) Botanical histochemistry. Freeman, San Francisco 19. Gahan PB (1984) Plant histochemistry and cytochemistry – an introduction. Academic, London 20. Yeung EC (1998) A beginner’s guide to the study of plant structure. In: Karcher SJ (ed) Tested studies for laboratory teaching, vol 19. Proceeding of the 19th workshop/conference of the Association for Biology Laboratory Education (ABLE). Purdue University, Lafayette, IN, pp 125–141

Chapter 9 Use of Statistics in Plant Biotechnology Michael E. Compton Abstract Statistics and experimental design are important tools for the plant biotechnologist and should be used when planning and conducting experiments as well as during the analysis and interpretation of results. This chapter provides some basic concepts important to the statistical analysis of data obtained from plant tissue culture or biotechnology experiments, and illustrates the application of common statistical procedures to analyze binomial, count, and continuous data for experiments with different treatment factors as well as identifying trends of dosage treatment factors. Key words: Analysis of variance, Binomial data, Concentration treatment factors, Continuous data, Count data, Data analysis, Logistic regression, Mean separation tests, Plant tissue culture, Poisson regression, Regression analysis

1. Introduction Most research projects are initiated to solve a problem. In response, we plan and design experiments in the hope that some treatment will be found that solves the problem. Researchers use a logical and stepwise approach for problem solving. We examine the published literature to gain knowledge from prior experiences and apply what we have learned to formulate a hypothesis. Experimental objectives are developed that can be tested objectively and data gathered from observations made during experimentation. Finally, data are analyzed and evaluated to ascertain the effectiveness of each treatment at correcting the problem. We can easily make measurements of plant cells and tissues, and mathematically calculate and rank the averages of the tested treatment variables. However, simply calculating averages does not consider the variation present among specimens receiving the treatments and does not accurately examine treatment effectiveness.

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_9, © Springer Science+Business Media, LLC 2012

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There are many statistical procedures that can be used to measure variation within and between treatments and provide us a better estimate of treatment effectiveness. For this reason statistics should be employed when evaluating data. It is important that we avoid personal bias during all phases of experimentation. Personal bias, either occurring intentionally or by accident, will produce unreliable results that will inhibit the researchers’ attempts to solve problems. Various experimental designs such as the completely randomized (CR), randomized complete block (RCB), incomplete block (IB), and split plot (SP) have been developed to help researchers reduce personal bias during experimentation and data collection (1–3). For more information on how these designs are used in plant biotechnology the readers should consult prior publications (4–6). Use of the most appropriate and efficient statistical procedures can aid researchers in planning, conducting, and interpreting experimental results. This chapter is intended to serve as an introduction to the use of statistics in plant biotechnology research. After reading this chapter the reader should be able to select the appropriate statistical methods to analyze, interpret, and present plant biotechnology data.

2. Materials 2.1. Computer Software Used to Perform Statistical Analyses

In this day and age few plant biotechnologists calculate statistical analyses by hand or use a calculator. Instead, most scientists choose to use a statistical software package that is compatible with their personal computer (PC). Several windows-compatible software packages are available for statistical analysis procedures using a PC and include those available from SAS (7), SPSS (8), SYSTAT (9), MINITAB (10), and STATISTX (11). All software programs can be used to efficiently perform data analysis procedures used for plant cell and tissue culture and plant molecular biology data. To illustrate the use of statistical procedures commonly used in plant biotechnology, two hypothetical experiments are used. The first evaluates the effectiveness of six cytokinins [zeatin, zeatin riboside, N6-(δ2-isopentenyl)-adenine (2iP), benzyladenine (BA), kinetin, or thidiazuron (TDZ)] on stimulating adventitious shoots from petunia leaf explants while the second was designed to identify the optimum BA dose required for shoot organogenesis in petunia. The hypothetical data collected included the number and percentage of explants that produce shoots, the number of shoots per responding explant, and the length of adventitious shoots.

2.2. Plant Materials

Plants of Petunia × hybrida “Blue Picotee” were grown from seed in the greenhouse for 12 weeks before excising leaves for explant preparation. Only the youngest, fully expanded leaves were harvested.

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Plants were grown at 20°C and natural light intensities and photoperiod at Platteville, WI, from September to March. The freshest quiescent seeds should be obtained. Seeds can be stored at 4°C for about 5 years and remain regenerable. 2.3. Shoot Regeneration Medium

Petunia Shoot Regeneration Medium: MS salts and vitamins with (per liter) 0.1 g myo-inositol, 30 g sucrose, and 5 g agar-gel (Phytotechnology Laboratories, LLC, Overland Park, KS) at pH 5.8 (12). The plant growth regulators tested included zeatin, zeatin riboside, 2iP, benzyladenine, kinetin, or TDZ. All growth regulators were obtained from Phytotechnology Laboratories, LLC, Overland Park, KS, and supplied at 0, 2, 4, 6, 8, or 10 μM concentrations, respectively.

3. Methods 3.1. Explant Preparation and Culture Conditions

The methods used for explant preparation were outlined previously by Preece (12). The youngest, fully expanded leaves were removed from plants actively growing in the greenhouse. Leaves were washed with soapy water and immersed in a 10% bleach solution (0.6% NaOCl with 1 ml/l antibacterial soap) for 15 min before three rinses with sterile reverse osmosis water. To prepare the explants, the margins were trimmed from disinfested leaves and the lamina cut into 5 × 5-mm explants, each containing a portion of the midrib. Explants were placed abaxial side down in test tubes containing 20 ml of shoot induction medium supplemented with test concentrations of the selected cytokinins. One leaf explant was cultured per vessel. Test tubes containing explants were incubated in a growth chamber providing a 16-h photoperiod (30–50 μmol/m2 s) and 25°C. Test tubes containing explants were selected at random and placed in racks that held 32 vessels. All racks were placed on the same shelf in the growth room and arranged in a completely randomized design (see Note 1). Explants were transferred to vessels containing 20 ml of fresh shoot induction medium every 4 weeks.

3.2. Statistical Analysis Procedures

Statistix for Windows© (see Note 2) was used to analyze the experimental data. Like other windows-based versions of statistical software, Statistix for Windows© uses drop-down dialog boxes to guide the user through data analysis (11). The following paragraphs are divided into sections demonstrating the use of statistical analysis software to analyze binomial,

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count, and continuous data for experiments with different treatment factors as well as identifying trends of dosage (concentration) treatment factors. Explants were placed in treatment media described above. Data for all experiments were recorded at 12 weeks and included the number and percentage of explants with shoots, the number of shoots per responding explant, and the length of each shoot recorded. Data analysis procedures were performed based on a completely randomized design with one replicate per vessel, making each explant a replicate (see Note 3). Vessels were randomly placed into racks positioned on the same shelf in the growth chamber. Therefore, the model statements used for each analysis were constructed to reflect a completely randomized design. 3.3. Analysis of Binomial Data

Logistic regression is the statistical procedure suggested for analyzing response data (13). This is because, unlike ANOVA, logistic regression does not produce separate estimates of experimental error. Because of this feature, logistic regression produces more accurate results than ANOVA when analyzing response data. The logistic regression procedure can be found in Statistix for Windows© in the linear models selection of the statistics drop-down menu. The following steps should be followed when using this software to conduct logistic regression analysis. While working in the appropriate data file, select the “Statistics” drop-down menu in the tool bar and click on “Linear Models.” This action creates a new box listing several linear model-based procedures, one of which is logistic regression. Clicking on “Logistic Regression” produces a new window containing boxes in which the dependent and independent variables must be entered. In this example, the dependent variable is “response” and the independent variable is cytokinin. Click OK after entering names of the requested variables. Clicking the OK button initiates the analysis. Test results appear in a new window that can be printed or saved. When reading the analysis output, significance of the independent variable, cytokinin type in this case, is indicated by the P value (see Note 4).

3.4. Analysis of Count Data

Data, such as the number of shoots produced per regenerating explant or number of somatic embryos per explant, are considered counts (13). Count data are not normally distributed because the variance of each treatment is equal to the average response of the treatment (14). Because of their distribution, Poisson regression (also known as discrete regression) is suggested for analyzing count data (13). The advantage of Poisson regression is that the procedure uses a logarithmic value of the mean counts, which normalizes the data during analysis (13). The following steps should be followed when using Statistix to conduct Poisson regression analysis.

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While working in the appropriate data file, select the “Statistics” drop-down menu and click on “Linear Models.” This creates a new box listing several linear model-based procedures, one of which is Poisson regression. Clicking on Poisson regression produces a new window in which the dependent and independent variables must be entered. In this example, the dependent variable is the number of shoots (NOSHOOTS) and the independent variable is CYTOKININ. Click on the OK button after entering the information. Clicking the OK button initiates the analysis. Test results appear in a new window that can be printed or saved. When reading the analysis output, significance of the independent variable, cytokinin type in this case, is indicated by the P value (see Note 5). 3.5. Analyzing Continuous Data

The shoot length variable is considered continuous since the value of data observations is unrestricted. Because of this fact, continuous data tend to be normally distributed with treatments having similar variances (13). ANOVA is well suited for analyzing continuous data with a normal distribution (4, 5, 13). During ANOVA, a model statement is created that identifies the treatment variables and the observations recorded (dependent variables) as well as treatment interactions (independent variable), if present. The model statement must be written based on the experimental design used (4). The procedure generates a random error value by subtracting the value of each datum from the overall mean (13). The influence of independent variables on the dependent variables is tested according to the model statement, generating a summary table that provides the results of the model tested (2). Information in the summary table includes the degrees of freedom (DF), sources of variation (SS), mean square error (MSE) F-statistic (F), and estimates the probability (P) value that determines the level of significance of the F-statistic (2). The following steps should be followed when conducting a general ANOVA using Statistix. While working in the appropriate data file, move the cursor to the “Statistics” drop-down menu. Clicking on “Linear Models” creates a new box listing several linear model-based procedures, one of which is the general ANOVA. Click on “GENERAL ANOVA” to display a new window in which the dependent variable must be entered. In this example, the dependent variable is shoot length (SHOOTSLTH). The model statement should be entered in the box identified as “AOV Model Statement.” In this case, the model statement is “CYTOKININ.” No other variables are entered into the model statement in this situation because cytokinin is the only treatment factor. If there were multiple treatment factors, each would be written in the model statement with the interactions of interest (see ref. 4 for instructions on writing model statements for experimental designs).

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Clicking the OK button initiates the analysis and the results appear in a new window that can be printed or saved. In ANOVA, the sources of variation are listed with their DF, SS, MS, F, and P values. In this example, there are two main sources of variation identified as the treatment factor (cytokinin type) and the residual (experimental error). When reading the analysis output, significance of the treatment factor (cytokinin type) is indicated by the P value (see Note 6). 3.6. Analyzing Treatment Means

Treatment means can be analyzed to determine treatment differences once a significant value is obtained in the preliminary statistical test (ANOVA, Poisson regression, or Logistic regression). A separate mean comparison evaluation test is not necessary when there are only two treatments because the general test (ANOVA, Poisson regression, or logistic regression) alone determines the statistical difference (4). However, most researchers evaluate multiple treatments simultaneously. The easiest way to compare treatment means is to rank them in ascending or descending order and pick the best one. However, this method does not measure variation within the treatments and may not, on its own, accurately represent how the explants responded to the treatments (13, 15). For this reason, it is suggested that a mathematical procedure that calculates within-treatment variation be used to compare treatment means. There are many mean separation procedures that account for within-treatment variation. The procedures most commonly used in plant biotechnology research to compare the means of unrelated or related treatments are multiple comparison and multiple range tests, standard error of the mean (SEM), and orthogonal contrasts.

3.6.1. Multiple Comparison and Multiple Range Tests

Multiple comparison and multiple range tests are statistical procedures that use the population variance to calculate a numerical value for comparing treatment means (4, 5, 15). Means are ranked in ascending or descending order and the difference between adjacent means calculated and compared to a value computed by the statistical test (13). The two treatment means are considered different if their difference exceeds the computed statistical value. However, if the difference between treatment means is equal to or less than the computed statistical value, the treatments are considered similar (13). Multiple comparison tests calculate one statistical value and use it to compare adjacent and nonadjacent means. Examples of multiple comparison tests are Bonferoni, Fisher’s least significant difference (LSD), Scheffe’s, Tukey’s Honestly Significant Difference Test (Tukey’s HSD), and Waller–Duncan K-ratio T test (Waller– Duncan). One problem with these procedures is that they may overestimate treatment differences among treatments ranked far apart. This occurs because treatment variances tend to increase with increasing data values (13). One should use caution if using

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one of the above procedures in experiments with a large number of treatments. Multiple range tests differ from multiple comparison tests because the former employs different critical values to compare adjacent and nonadjacent means (4). This modification improves the accuracy of the test, making it less likely that errors will be made when comparing distantly ranked means. Examples of multiple range tests include Duncan’s New Multiple Range Test (DNMRT), Ryan–Einot–Gabriel–Welsh Multiple F-test (REGWF), Ryan– Einot–Gabriel–Welsh Multiple Range Test (REGWQ), and Student Newman–Keuls (SNK). The Ryan–Einot–Gabriel–Welsh Multiple Range Test is recommended because of its moderate level of conservancy. Unfortunately, multiple range tests are not always available in PC statistical software packages. Mean comparisons are conducted as part of an ANOVA. The following steps demonstrate how to conduct the Tukey’s HSD test using Statistix. While working in the appropriate data file, select the “Statistics” drop-down menu and click on “Linear Models.” This creates a new box listing several linear model-based procedures, one of which is the general ANOVA. Clicking on “GENERAL ANOVA” produces a new window in which the dependent variable must be entered. In this example, the dependent variable is shoot length (SHOOTSLTH). CYTOKININ is written in the model statement box. Clicking the OK button initiates the test. The results are displayed in the general ANOVA coefficient table window. Clicking “Results” in the toolbar display a drop-down box listing procedures that can be used to evaluate treatment means or variances. Clicking on “Comparison of Means” displays a window listing various mean comparison tests. Enter the desired main effect, or interaction, to be tested (CYTOKININ in this case) and click on one of the available tests. In this case, the desired test is Tukey’s HSD. Click OK to initiate the test. An output is generated in a new window that lists the treatments and their means, the homogeneous groups and the number of significant groups, as well as the critical Q value and the critical value for comparisons. The means with their homogeneous group identification may then be displayed in a table or a graph (see Note 7). 3.6.2. Orthogonal Contrasts

Orthogonal contrasts are used to make comparisons between treatments with similar characteristics (4, 13). In plant tissue culture and biotechnology studies, these may be plant growth regulators (PGRs) with similar activity (e.g., natural vs. synthetic cytokinins) or DNA constructs with the same promoter. Orthogonal contrasts differ from mean comparison tests in that more than two treatments can be compared in one test. However, the number of

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comparisons made must be restricted to the number of degrees of freedom for the treatment variable (2). Orthogonal contrasts are performed as part of the ANOVA procedure (4). A contrast statement is written that specifies the treatments or group of treatments to be compared and the ANOVA procedure calculates the DF, SS, and MS for the comparison. An F statistic is calculated for the contrasts and the level of significance (P value) determined. One DF is used for each comparison. The following steps demonstrate how to perform orthogonal contrasts using Statistix. While working in the appropriate data file, select the “Statistics” drop-down menu. Click on “Linear Models” to create a new box listing several linear model-based procedures, one of which is the general ANOVA. Click on general ANOVA. In the ANOVA window, indicate the dependent variable and type in the model statement. Click OK to initiate the test. Click on “Results” located in the toolbar of the general ANOVA coefficient window. This generates a list of treatment evaluation procedures. Clicking on “General Contrasts” produces a new window in which the contrast main effect, or interaction, and appropriate contrast coefficients for the desired treatment, or treatment group, comparisons are entered (see Note 8). Clicking OK initiates the test and displays the results in a new window. The results are interpreted by identifying the level of significance (P value) for each contrast (see Note 9). 3.6.3. Standard Error of the Mean

The standard error (SE) is frequently used for mean comparison purposes in plant tissue culture and biotechnology research. SEs are obtained by dividing the sample standard deviation by the square root of the number of observations for that treatment (14). Many researchers use SE values like a mean comparison test, generating an individual value for each treatment and comparing the difference between the means of paired treatments with their calculated SE. The researcher often declares two treatments similar or different if the collective values (treatment mean ± its SE) for the paired treatments do not overlap. This use of SE can be used to compare means ranked adjacently. However, problems occur when using SE to compare means that are ranked far apart. When remembering how SE values are calculated, one would realize that SE values increase with the numerical value of the data, causing the researcher to overestimate treatment differences and violate the assumption of ANOVA that treatment variances are equal (13). Therefore, the use of SE to compare means ranked far apart fails to produce useful results and does not accurately reflect population variance. The following steps can be used to generate SE values for the accurate comparison of treatment means. This test is most valuable for treatments that are unrelated (5, 13).

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While working in the appropriate data file, select the “Statistics” drop-down menu and click on “Linear Models.” This creates a new box listing several linear model-based procedures, one of which is the general ANOVA. Click on general ANOVA. In the ANOVA window, indicate the dependent variable and type in the model statement. Click OK to initiate the test. Click on “Results” located in the toolbar of the general ANOVA coefficient window. This generates a list of treatment evaluation procedures. Select “Means and Standard Errors.” Enter the main effect, or interaction, and click OK to initiate the test and generate the results. The results are displayed in a window. The identity of treatment with its means and SS is listed as well as the number of observations per cell, the standard error of an average, and the standard error of the difference of two averages (see Note 10). 3.7. Dosage, or Concentration Treatments

Researchers that design experiments with treatments consisting of various doses or concentrations of a single treatment factor are usually interested in identifying a single dose, or concentration, that produces an optimal explant response. In other words, the researcher is interested in identifying a trend present among the levels of the treatment factors. The best statistical procedure for these types of experiments is usually trend analysis (5, 13). In trend analysis, models identifying specific trends (linear, quadratic, cubic) are tested in a stepwise fashion from simplest (linear) to most complex (cubic in most cases) until a nonsignificant trend is identified (16). The last significant trend is considered to best describe the response to the treatments. Trend analysis uses SS, T, and R2 values to indicate significant trends (4). Trends may be tested through regression analysis or polynomial contrast statements in ANOVA. The most effective method of conducting trend analysis depends on the experimental objectives and the statistical software package used. To illustrate trend analysis, the treatments for the petunia example can be changed from six cytokinin types to six concentrations of BA [0 (control), 2, 4, 6, 8, and 10 μM]. The objective of this experiment would be to identify a trend in explant response to BA that would identify an optimum concentration of the growth regulator for adventitious shoot organogenesis. Data recorded included the percentage of explants that produced shoots, number of shoots per explant, and length of regenerated shoots. The following steps can be used to conduct trend analysis using Statistix. For simple linear regression: While working in the appropriate data file, select the “Statistics” drop-down menu. Clicking on “Linear Models” creates a new box listing several linear model-based procedures, one of which is linear regression.

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Clicking on linear regression produces a window in which the dependent and independent variables must be entered in their respective boxes. Click OK after entering these variables. Clicking OK initiates the procedure and produces a window displaying the linear regression coefficient table (see Note 11). For trend analysis using polynomial contrasts: While working in the appropriate data file, select the “Statistics” drop-down menu and click on “Linear Models.” This creates a new box listing several linear model-based procedures, one of which is the general ANOVA. Clicking on general ANOVA window displays a box in which the dependent variable and type in the model statement must be entered. Enter the appropriate statements. Clicking on OK initiates the test and produces the ANOVA results with a new toolbar. Clicking on “Results” located in the toolbar of the general ANOVA coefficient window generates a list of treatment evaluation procedures. Selecting “Polynomial Contrasts” produces a new window in which the level of polynomial contrasts and the contrast main effect, or interaction, must be entered (see Note 12). Click on OK. Clicking on OK produces a window displaying the results of the polynomial contrasts for the desired dependent and independent variables indicated in the ANOVA. The last polynomial degree with a significant P value is considered to be the most significant trend (see Note 13).

4. Notes 1. Because one explant was cultured in a vessel and the vessels randomly placed in the test-tube rack, the experimental design was a completely randomized design (2). The CR design is commonly used for plant biotechnology experiments because it is easy to use and allows researchers to maximize the number of replicates examined as well as utilize either equal or unequal replication for the treatments (1). The CR design is also amenable to statistical procedures for binomial, count, continuous, and concentration data (5). These advantages are important as maximizing replicate numbers can lead to a more powerful test in determining treatment differences. Flexibility in the number of replicates for each treatment is important because unequal replication often occurs due to contamination or death of explants.

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Table 1 Results of analysis of variance of petunia shoot length data analyzed using a completely randomized design Source

SS

MS

F

P

5

1,803.35

360.67

12.46

700 μg Mn/g) by Markert (14). S. americanus root cultures are about twice more efficient to remove metals than T. latifolia roots. Both plant species capture metals in the following order: Cr > Pb > Mn.

4. Notes 1. Dissolving lead, chromium, or manganese salts in deionized water or culture medium promotes a light precipitation of metals. This effect is not observed when metals are dissolved in HNO3 0.02 M. 2. The concentration of lead, chromium, and manganese in certified water is: 19.63 ± 0.21 μg/L Pb2+, 20.40 ± 0.24 μg/L Cr3+, and 38.97 ± 0.45 μg/L Mn2+. Reference plant material

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contains: 0.87 ± 0.03 μg/g Pb2+, 1 ± 0.05 μg/g Cr3+, and 98 ± 3 μg/g Mn2+. 3. Due to the reaction between its components, aqua regis quickly loses its effectiveness. Therefore, its components should be mixed immediately before use. In order to pour the mixture into the sink, first carefully neutralize it with sodium bicarbonate. 4. The PPM is the best choice for asepsis of roots; however, this product is not currently easily available. An optional asepsis includes the following: (a) immersion of root in a biocide mixture (3 g/L benlate, 3 g/L captan, 1 mL/L previcur, 0.5 g/L amoxicilin and 0.4 g/L ketoconazol) for 24 h; (b) treatment with 10% benzalkonium chloride for 24 h; (c) disinfection with 5% (v/v) commercial sodium hypochlorite (Cloralex®, Allen) for 10 min and 70% ethanol for 2 min. It is quite important to wash the roots immediately after treatment with hypochlorite. 5. It is recommended to verify the instrument response with known standards. For the quality control of the metal analysis, determine the levels of Pb, Cr, and Mn in the reference water and plant material. The metal recovery should range between 90 and 110% of certified concentration in the reference material. References 1. Manios T et al (2003) The effect of heavy metals accumulation on the chlorophyll concentration of Thypha latifolia plants, growing in a substrate containing sewage sludge compost and watered with metaliferus water. Ecol Eng 20:65–74 2. Pilon-Smits E, Pilon M (2002) Phytoremediation of metals using transgenic plants. Crit Rev Plant Sci 21:439–456 3. Lasat MM (2002) Phytoextraction of metals: a review of biological mechanisms. J Environ Qual 31:109–120 4. Ghosh M, Singh SP (2005) A review on phytoremediation of heavy metals and utilization of its byproducts. Appl Ecol Environ Res 3:1–18 5. Nedelkoska TV, Doran PM (2000) Hyperaccumulation of cadmium by hairy roots of Thlaspi caerulescens. Biotechnol Bioeng 67:607–615 6. Macek T et al (1994) Accumulation of cadmium by hairy-root cultures of Solanum nigrum. Biotechnol Lett 16:621–624 7. Subroto et al (2007) Accumulation of zinc by hairy root cultures of Solanum nigrum. Biotechnology 6:344–348 8. Maitani et al (1996) The composition of metal bound to class III metallothionein (phytochelatin and its desglycyl peptide) induced by various

metals in root cultures of Rubia tinctorum. Plant Physiol 110:1145–1150 9. Boominathan R, Doran P (2002) Ni-induced oxidative stress in roots of the Ni hyperaccumulator, Alyssum bertolonii. New Phytol 156:205–215 10. Santos-Díaz et al (2007) Induction of in vitro roots cultures of Thypha latifolia and Scirpus americanus and study of their capacity to remove heavy metals. Electronic J Biotechnol 10:417–424 11. Santos-Díaz MS, Barrón-Cruz MC (2011) Lead, chromium and manganese removal by in vitro root cultures of two aquatic macrophytes species: Typha latifolia L. and Scirpus americanus Pers. Int J Biorem 13:538–551 12. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497 13. Espinoza-Quiñones et al (2005) Removal of heavy metal from polluted river water using aquatic macrophytes Salvinia sp. Braz J Phys 35:744–746 14. Markert B (1992) Presence and significance of naturally occurring chemical elements of the periodic system in the plant organism and consequences for future investigations on inorganic environmental chemistry in ecosystems. Vegetatio 103:1–30

Chapter 21 Establishment of a Sanguinarine-Producing Cell Suspension Culture of Argemone mexicana L (Papaveraceae): Induction of Alkaloid Accumulation Felipe A. Vázquez-Flota, Miriam Monforte-González, Cecilia Guízar-González, Jorge Rubio-Piña, and Karen Trujillo-Villanueva Abstract A protocol for the induction of a cell suspension culture of Argemone mexicana is described. This suspension has been kept for over 3 years producing sanguinarine, a benzophenanthridine-type alkaloid. Sanguinarine levels can be increased by exposing these cultures to yeast or fungal elicitation. Key words: Argemone mexicana, Benzophenanthridine, Elicitation, Sanguinarine, Secondary metabolism

1. Introduction Sanguinarine is a benzophenanthridine-type alkaloid produced by some Papaveraceae plants, where it is mainly accumulated in underground tissues (1). It displays toxic effects since it can be intercalated into DNA, due to its planar structure. Furthermore, its cationic nature allows it to bind to negatively charged membranes, and its reactivity toward thiol groups interferes with a number of cytosolic enzymes (2). Given these toxic properties, sanguinarine is considered part of the plant chemical arsenal against microbes and herbivores (3). In cell cultures, sanguinarine accumulation is frequently induced upon exposure to different chemical and biological elicitors, such as jasmonates and microbial homogenates (4). This response has been shown to be preceded by the transcriptional activation of several sanguinarine biosynthetic genes, including

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_21, © Springer Science+Business Media, LLC 2012

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tyrosine decarboxylase (TyDC), norcoclaurine synthase (NCS), berberine bridge enzyme (BBE), among others (1). We have developed a cell suspension culture of Argemone mexicana L. (Papaveraceae; common name: prickly poppy), which produces sanguinarine in significant amounts, even in the absence of any induction treatment. Maximal sanguinarine accumulation in this A. mexicana cell suspension culture (named AMMFi) is near to 3.0 mg/g DW, which is in the same magnitude order as those from other sanguinarine producing cultures after exposure to conditions that induce secondary metabolism (4). Interestingly, treatment of this A. mexicana cell culture with chemical inducers, such as jasmonate or salicylic acid, resulted in a limited increase of sanguinarine content (5). The operation of a sanguinarine detoxification mechanism has been proposed to limit any further increase in these cultures (2, 5). Since plant cell defense responses may evoke the participation of different, although convergent, signaling pathways (6), the exposure to single inducers may not be enough to trigger a full response. Hence, the use of elicitors prepared from cell-free pathogenic microorganism cultures could overcome such limited induction response. These preparations represent complex mixtures of organic compounds, which potentially may trigger the different signaling pathways. The former part of this chapter describes a protocol for the induction and maintenance of a sanguinarine-producing cell suspension culture of A. mexicana. In the latter part, the development of a methodology to induce sanguinarine accumulation in this cell suspension is described.

2. Materials All media for plant cells must be prepared with deionized water and based on the Phillips and Collins’ medium (PC) (7), supplemented with 25 g/L sucrose and adjusted to pH 5.8. For the maintenance of the Fusarium oxysporum (see Note 1) culture, potato–dextrose–agar (PDA; Sigma-Aldrich Chemical Co., St. Louis MO) is recommended. 1. Naphthaleneacetic acid (NAA) and 6-benzyladenine (BA), 1.0 mg/mL stocks: Dissolve 100 mg NAA or BA in a 10 mL of 0.1 N KOH and adjust volume to 100 mL with water. 2. Methyl jasmonate (MeJa) 10 mM stock: dilute 22.9 μL of MeJa (95%, ρ = 1.030 g/mL; Sigma-Aldrich Chemical Co.) in a total volume of 10 mL of ethanol. Sterilize the solution by filtration using 0.2 μm pore size nylon sterile membranes (Corning, NY).

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3. Salicylic acid (SA) 10 mM stock: 13.8 mg of SA (99% SigmaAldrich Chemical Co.) in 5 mL of ethanol and adjust volume to 100 mL with water. Sterilize the solution by filtration using 0.2 μm pore size nylon sterile membranes (Corning, NY). 4. Yeast extract (YE) 400 g/L stock: 2.0 g of YE (Sigma-Aldrich Chemical Co.) dissolved in 5 mL of water. Sterilize the solution by filtration using 0.2 μm pore size nylon sterile membranes (Corning, NY). 5. Sanguinarine 10 ng/μL reference solution: 1 mg of sanguinarine hydrochloride (Sigma-Aldrich Chemical Co.) is dissolved in 1 mL with methanol and 10 μL of this solution is diluted to 1 mL with methanol (see Note 2).

3. Methods 3.1. Induction of Cell Suspension Cultures

Cell suspension cultures are initiated from A. mexicana leaf callus. 1. Collect leaves around 5 cm long from mature plants and soak them in soapy water for 30 min, rinse with tap water and blot on paper towels. Disinfest the exscinded leaves by subsequent washes in 70% ethanol (3 min), 0.6% of sodium hypochlorite (15 min) and sterile distilled water. Carry out these operations under aseptical conditions (using a laminar air flow cabinet). 2. Cut leaves in 1.0 cm2 squares and culture on semisolid PC medium, supplemented with 0.5 and 1.5 mg/L BA and NAA, respectively (hereafter called PC-BN medium). Incubate the tissues at 25 ± 2°C under continuous light (photon flux density of 40–60 μmol/m2 s), provided by fluorescent lamps (39 W Philips Alto collection, Philips of México, México). After 4 weeks, separate calli formed on explants and transfer them to fresh PC-BN media. 3. Induce cell suspensions by transferring friable calli to PC-BN liquid medium. Maintain suspensions through biweekly subcultures, under continuous illumination and shaking (100 rpm).

3.2. Preparation of the F. oxysporum Cell-Free Homogenate

1. Use 30 day-old F. oxysporum PDA plate cultures (see Note 1) to initiate liquid cultures. Briefly, transfer sections of mycelium (1 cm2) to 50 mL of PC media without growth regulators and incubate during 6 days at 22°C in the dark and with rotatory shaking (120 rpm). 2. Homogenize mycelia and media with a polytron (JankeKunkel, T2) for 2 min, autoclave at 1 kg/cm2 for 30 min, and subsequently centrifuge under sterile conditions. Use the supernatant as elicitor (4, 5) and keep it in the dark at 4°C.

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3.3. Induction Procedures

Ten-day-old cell cultures, in the active growth phase, are used in all experiments. 1. Add 5 mL of the A. mexicana cell suspension (containing between 0.20 and 0.22 g fresh weight/mL) to a 250-mL Erlenmeyer flask, containing 50 mL of PC-BN medium and cultivate for 10 days, as described in previous sections. 2. On the 10th day of culture, induce suspensions by adding either 550 μL of the MeJa, SA or 500 μL of YE stock solutions. These volumes will render final concentrations of 100 μM for MeJa and SA, and 200 mg/L for YE. Also induce cultures with 500 μL of the cell-free F. oxysporum homogenate (final dose 30 mg of glutamate equivalents/L). Mock-induce controls with 500 μL of water. 3. Collect samples (triplicates) after 0, 24, 48, 72, 96, and 120 h of exposure to the elicitors. Collect cell package by filtration, weigh, freeze in liquid nitrogen, and keep at −80°C until analysis. Keep spent media for analysis (see Note 3).

3.4. Alkaloid Extraction and Quantification

Alkaloids are extracted from freeze-dried tissues and quantified by densitometry after separation by thin layer chromatography (TLC), as reported previously (5). 1. Homogenize 100 mg of freeze-dried tissue with 10 mL of HCl 0.5% in methanol (v/v) and incubate 2 h at 45°C with gently shaking. Separate and eliminate cell debris by filtration and reduce extract volume to dryness at low pressure. Dissolve residue in 1 mL of methanol. 2. Load between 1 and 2 μL of the extract on silica gel 69 F254 chromatography plates (aluminum supported; Merk Damstadt Germany). 3. In the same plate, load 1 μl of the sanguinarine dilutions so that a reference plot from 1 to 10 ηg is built (see Note 2). 4. Separate alkaloids on the TLC plate using a mobile phase of n-buthanol–acetic acid–water (7:1:2 by vol.) (see Note 4). 5. After chromatography, allow solvent to evaporate and visualize alkaloids on the plate using long wave UV light (365 nm). Sanguinarine is identified as a fluorescent red-orange spot with Rf value of 0.52 in this system. 6. Quantify sanguinarine on the plates by in situ densitometry using a Shimadzu CS-930 dual wavelength chromatoscanner, equipped with a DR 2 data collector (Kyoto Japan). Set absorbance to 465 nm. Contents of sanguinarine in the A. mexicana cell cultures are comparable to those of plant roots (Table 1). Although elicitation with F. oxysporum and YE can double these amounts,

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Table 1 Maximal accumulation of sanguinarine in A. mexicana cell suspension cultures exposed to different agents Treatment

Time of exposure (h)

Sanguinarine content (mg/g DW)

Control

–a

0.96 (0.11)

Methyl jasmonate

72

2.13 (0.17)

a

1.06 (0.83)

Salicylic acid

–

Yeast extract

48

3.2 (0.36)

F. oxysporum homogenate

96

3.8 (0.41)

Average of triplicates with standard deviation between brackets a Sanguinarine contents were kept without significant variation throughout the experiment

they were still at the same magnitude order than those in plants (Table 1). Culture response to MeJa is limited, whereas SA does not produce any response (Table 1). Argemone mexicana is one of the few species able to accumulate both sanguinarine (a benzophenanthridine) and berberine (a protoberberine). However, berberine is not detected in undifferentiated cultures of this plant, even under induction conditions of secondary metabolism (5). Though, the need of cell organization is well documented for the biosynthesis of several alkaloids, it is not required for the synthesis of this alkaloid in in vitro cultures from other berberine producing species, such as Berberis stolinifera, Coptis japonica, and Thalictrum flavum (1). Comparing alkaloid metabolism in the A. mexicana cell cultures to those of different plant tissues may establish the basis for this restriction.

4. Notes 1. The F. oxysporum strain was isolated from a Capsicum chinense plantation located in Cuzamá Yucatán (20°44¢29″ N 89°19¢6″ W; Islas-Flores collection Ref. FPACF4, Centro de Investigación Científica de Yucatán). 2. The equation relating sanguinarine to optical density is y = 5,282x − 544, where y is the amount of sanguinarine in nanogram and x is the optical density at 465 nm. Linear response can be obtained up to 150 ng.

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3. Cultures should be continuously monitored during the induction treatment, since occasionally a darkening reaction could develop. If it is detected, allow cell package to settle down and observe media color. A reddish coloration indicates sanguinarine excretion to the media, whereas a brownish one may be related to phenol production. Being this the case, it is recommended to stop the treatment and collect cells shortly after, since it frequently precedes cell death. Use this information to adjust the conditions for the induction treatment, whether by using lower doses or shorter exposure times. 4. The separation obtained in 5-cm plates is sufficient to avoid overlapping of sanguinarine with other alkaloids present in the extract. References 1. Ziegler J, Facchini P (2008) Alkaloids biosynthesis: metabolism and trafficking. Annu Rev Plant Biol 59:735–769 2. Weiss D, Baumert A, Vogel M, Roos W (2006) Sanguinarine reductase, a key enzyme of benzophenanthridine detoxification. Plant Cell Environ 29:291–302 3. Chang CY, Chang RF, Khalil TA, Hsieh WP, Wu CY (2003) Cytotoxic benzophenanthridine and benzylisoquinoline alkaloids from Argemone mexicana. Z Naturforsch 58c: 521–526 4. Eilert U, Kurz WGW, Constabel F (1985) Stimulation of sanguinarine accumulation in

Papaver somniferum cell cultures by fungal elicitors. J Plant Physiol 119:65–76 5. Trujillo-Villanueva K, Rubio-Piña J, MonforteGonzález M, Vázquez-Flota F (2010) Fusarium oxysporum homogenates and jasmonate induce a limited sanguinarine accumulation in Argemone mexicana cell cultures. Biotechnol Lett 32:1005–1009 6. Maleck K, Dietrich R (1999) Defense on multiple fronts: how do plants cope with diverse enemies? Trends Plant Sci 4: 215–219 7. Phillips GC, Collins GB (1979) In vitro tissue culture of selected legumes and plant regeneration from callus cultures of red clover. Crop Sci 19:59–64

Chapter 22 Epigenetics, the Role of DNA Methylation in Tree Development Marcos Viejo, María E. Santamaría, José L. Rodríguez, Luis Valledor, Mónica Meijón, Marta Pérez, Jesús Pascual, Rodrigo Hasbún, Mario Fernández Fraga, María Berdasco, Peter E. Toorop, María J. Cañal, and Roberto Rodríguez Fernández Abstract During development of multicellular organisms, cells become differentiated by modulating different programs of gene expression. Cells have their own epigenetic signature which reflects genotype, developmental history, and environmental influences, and it is ultimately reflected in the phenotype of the cells and the organism. However, in normal development or disease situations, such as adaptation to climate change or during in vitro culture, some cells undergo major epigenetic reprogramming involving the removal of epigenetic marks in the nuclei followed by the establishment of a different new set of marks. Compared with animal cells, biotech-mediated achievements are reduced in plants despite the presence of cell polypotency. In forestry, any sustainable developments using biotech tools remain restricted to the lab, without progressing to the field for application. Such barriers in the translation between development and implementation need to be addressed by organizations that have the power to integrate these two fields. However, a lack of understanding of gene regulation is also to blame for this barrier. In recent years, great progress has been made in unraveling the control of gene expression. These advances are discussed in this chapter, including the possibility of applying this knowledge in forestry practice. Key words: Aging, Animals, DNA methylation, Histone modification, In vitro tissue culture, Plants, RNAi

1. Introduction During development of multicellular organisms, cells become differentiated by modulating different programs of gene expression (1). Environmental adaptation coincides with changes in the expression of genes that play a role in the stress response. The spatial and temporal regulation of gene expression is extremely Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_22, © Springer Science+Business Media, LLC 2012

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accurate in cells and tissues, being stable during the adaptation but not static, since expression can be reverted when the stimulus ends. One of the mechanisms that regulate gene expression meeting the characteristics described above is epigenetics, which can be defined as heritable changes in the phenotype caused by mechanisms other than changes in the DNA sequence, usually affecting gene expression. Each cell has its own epigenetic signature which reflects genotype, developmental history, and environmental influences, and it is ultimately reflected in the phenotype of the cell and the organism. However, in normal development or under adverse environmental conditions, such as those related to climate change or in vitro culture, some cells undergo major epigenetic reprogramming involving the removal of epigenetic marks in the nucleus followed by the establishment of a different new set of marks (2). The initiation of new cell fates as well as cell reprogramming to accomplish a new organogenic pathway or to adapt to climate change involving the establishment of distinct cell lines, are both accomplished by changes in the epigenetic marks. These changes normally consist of posttranslational modifications of the core nucleosome histones and transient changes in global DNA methylation, which ultimately determine gene expression reprogramming, which is manifested at the transcriptome, proteome, and metabolome levels. Although genetic variation plays a role in adaptation to new conditions and the absence or presence of alleles contributes to the surviving phenotypes, the crucial issue is how gene expression is controlled in genetically identical cells. Until now, this has remained an enigma how genetically identical cells of an organism differentiate and reprogram, maintaining strict spatial–temporal coordinates. Plant cell differentiation is the result of different microenvironments in genetically identical nuclei. Therefore, we will not be able to fully understand the genetic expression simply by considering the nucleotide and amino acid sequence information, without taking into account any modification of transcription or translation. Thus, the epigenetic code includes genetic information and the biochemical modifications that take place on the chromatin (3, 4). During cell differentiation or a metabolic switch, cells undergo profound changes in gene expression. These events are accompanied by complex modifications of chromosomal components and nuclear structures, including covalent modifications of DNA and chromatin up to topological reorganization of chromosomes and genes in the nucleus. To various extents, all these levels of organization appear to contribute to the stability and heritability of transcription programs and define what is meant as the epigenetic control of gene regulation. Most recent data suggest that tissue regeneration and transdifferentiation are controlled by epigenetic functions (5). Thus, the epigenome also provides the molecular basis for the preservation and plasticity of cell identity.

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2. Chromatin Regulatory Factors The chromatin is the form in which DNA is packaged within the eukaryotic cell. Its fundamental unit is the nucleosome, which consists of 146 bp of DNA wrapped around an octamer of core histones, each containing two molecules of H2A, H2B, H3, and H4. The function of this complex is to provide structure (i.e., packaged DNA to fit within the nucleus) and assist in the regulation of gene expression. Far from static, the chromatin structure is very dynamic, both spatially and temporally. This dynamism stems from the properties of the components (DNA and proteins), which are susceptible to a large number and type of biochemical modifications at different sites. These biochemical modifications are DNA methylation and posttranslational modifications (PTMs) of histones and are known as epigenetic marks, which are heritable and may be partly related to specific physiological states and stages. 2.1. DNA Methylation in Plants

DNA deoxycytosine methylation is the methylation of the 5¢ carbon of the pyrimidine ring of the cytosine (5-mdC). To date this is the only identified DNA epigenetic mark (6, 7). While in mammals it is restricted to CG sites, in plants it also occurs at CNG and CNN sites, where N is any base but G. Establishment and maintenance of DNA methylation is carried out by DNA methyltransferases (DNMTs), which catalyze the transfer of methyl groups donated by S-adenosyl methionine (SAM) to deoxycytosines and are more abundant in plants than in mammals. This, together with the existence of a greater number of sequences susceptible to methylation, allows plants a finer regulation. It is thought that this is a necessity associated with their sessile life form, which restricts them from fleeing adverse conditions. In plants, DNMTs are classified in four distinct gene families (8): 1. MET: This is the most extensively studied of the four gene families in plants. The methyltransferases of this family are responsible for maintenance of methylation especially at CG sites, but also are likely to play a role in maintenance of nonCG sites, as mutant studies indicate (6). Therefore, this family is crucial in epigenetic inheritance and imprinting. It is the homologous group to the DNMT1 family of mammalian methyltransferases. 2. DRMs encoding domain rearranged methyltransferases: These genes are similar to the mammalian DNMT3 family. Their function is to establish de novo DNA methylation, both CG and non-CG, in the RNA-dependent DNA methylation (RdDM) pathway (9). Thus, this family is very important in the defense against virus infection and in the response to environmental stimuli.

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3. CMTs encoding chromomethylases, which are plant-specific. Like DRMs, CMTs also catalyze DNA methylation in non-CG sequences, but are only responsible for their maintenance, not for their de novo methylation. 4. DNMT2: the role of this gene family in DNA methylation remains un-elucidated (8). Removal of DNA methylation is thought to occur in two different ways: replacement of methylcytosines by nonmodified cytosines during DNA replication (passive demethylation) and/or methylcytosines demethylation by DNA glycosylases (active demethylation). Two DNA glycosylases have been reported to date in plants: DEMETER (DME) and ROS1. Recently, a protein ROS3 containing an RNA recognition motif has been found to bind to ROS1. This may be evidence of the existence of a RNA-directed demethylation, possibly as part of the RdDM pathway (10). Until recently, DNA methylation was considered as a gene silencing mechanism. However, nowadays it is seen as a general gene regulation mechanism (i.e., responsible for both downregulation and upregulation of gene expression) and not independent, but as part of a more complex network (11). Therefore, there are strong indications that DNA methylation has an important role in the regulation of gene expression levels, making it pivotal in plant development and the physiological response to changing environmental conditions. Clusters of sequences susceptible to methylation, especially CG and CNG, are called methylation islands. They are most often found in association with promoters and first exons, but are less common in 3¢ regions of genes. The presence of 5-mdC in these regions is usually associated with gene silencing, but the effect is different. Thus, 5-mdCs in the promoter regions are more efficient in repressing gene transcription than those in the coding regions (12). The number of genes regulated by promoter methylation is large in plants. Recent studies have determined that methylation in promoter regions takes place at CG sites and depends on MET1 for maintenance and DRM2 for de novo methylation through RdDM (13). The role of DNA methylation in other gene regions are thought to be less determinant in regulation of gene expression, but actually remains unknown (14). Although the mechanism of DNA methylation is not completely known, it is well established that it can induce further chromatin remodeling by recruitment of methylcytosine-binding proteins such as KRYPTONITE (KYP), histone H3 (H3K9), and VARIANT IN METHYLATION 1 (VIM1), which affect the access of the transcription machinery to DNA, i.e., gene expression (15). 2.2. siRNA

RNA-directed DNA methylation (RdDM) is a nuclear process in which small interfering RNAs (siRNAs) direct the cytosine methylation of DNA sequences that are complementary to the siRNAs.

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In plants, double stranded-RNAs (dsRNAs) generated by RNAdependent RNA polymerase 2 (RDR2) serve as precursors for Dicer-like 3 (DCL3)-dependent biogenesis of 24-nt siRNAs. Plant specific RNA polymerase IV (Pol IV) is presumed to generate the initial RNA transcripts that are substrates for RDR2. siRNAs are loaded onto an argonaute4-containing RISC (RNA-induced silencing complex) that targets the de novo DNA methyltransferase DRM2 to RdDM target loci. Nascent RNA transcripts from the target loci are generated by another plant-specific RNA polymerase, Pol V, and these transcripts help recruit complementary siRNAs and the associated RdDM effector complex to the target loci in a transcription-coupled DNA methylation process. Small RNA binding proteins such as ROS3 may direct target-specific DNA demethylation by the ROS1 family of DNA demethylases. Chromatin remodeling enzymes and histone-modifying enzymes also participate in DNA methylation and possibly demethylation. One of the wellstudied functions of RdDM is transposon silencing and genome stability. In addition, RdDM is important for imprinting, gene regulation, and plant development. Locus-specific DNA methylation and demethylation, and transposon activation under abiotic stresses suggest that RdDM is also important in stress responses of plants (16). 2.3. Posttranslational Modifications of Histones

As described above, chromatin is a structural and functional complex formed by DNA and proteins, of which the core histones (H2A, H2B, H3, and H4) are the most prominent. Once translated, the core histones are susceptible to a number of biochemical modifications that are known as posttranslational modifications (PTMs) and include methylation, phosphorylation, acetylation, ubiquitination, glycosylation, sumoylation, biotinylation, carbonylation and ADP ribosylation, deimination, and proline isomerization (17). Core histones are globular proteins, but have an N-terminal tail, in which the PTMs occur most frequently. Therefore, core histones constitute a complex platform for modulating the access of the transcription machinery to chromatin. As various modifications can occur simultaneously in a nucleosome (i.e., at the N-terminal histone tails), these create a specific chromatin transcriptional environment. The set of PTMs that modulate the nucleosome landscape is known as the histone code. Each type of histone PTM is moderated by two enzymes: one that performs the modification and one that counteracts. Enzymes have been identified for acetylation, methylation, phosphorylation, ubiquitination, sumoylation, ADP-ribosylation, deimination, and proline isomerization (17). Although a transcriptional state depends on the set of PTMs in the nucleosomes, some individual PTMs have been established as primarily responsible. Lysine acetylation is thought to co-occur with transcription activation. The lysine acetylation neutralizes the basic charges and, as a consequence, chromatin becomes unfolded. This modification depends on two antagonistic enzyme families: histone acetyl transferases (HATs) and histone deacetylases

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(HDACs). In the model plant Arabidopsis thaliana, approximately 15 HATs have been described, classified into several families such as the GNAT, the CBP/p300, and the TAFII family (12). Meanwhile, HDACs in plants belong to three families: RDP-like, HD-tuin, and sirtuin (12). Histone lysine methylation is the most abundant form of histone modification. It is mediated by histone lysine methyltransferases (HKMT families) and, until recently, was thought to be an irreversible modification. However, recent experimental results have shown that enzymes such as FLOWERING LOCUS D (FLD), LSD1-LIKE 1 (LDL1), and LSD1-LIKE 2 (LDL2), involved in the regulation of plant flowering, are histone demethylases (12). Each lysine residue can be mono-, di-, or trimethylated by HKMTs. Lysine trimethylation at H3K4, H3K36, and H3K78 is an epigenetic mark of actively transcribed euchromatin, while trimethylation of H3K9, H3K27, and H4K20 is associated with transcriptional repression and implicated as mediators in the formation of silent heterochromatin (17). Although the above is generally accepted, it is necessary to point out that the effect of these and other histone PTMs depends on the gene region in which they occur. For example, methylation of H3K36 has a positive effect on transcription when occurring in the coding region and a negative effect when in the promoter. Methylation of H3K9 may have the same effect: restrictive in the promoter and promoting in the coding region (6). These examples make clear that PTMs are not unidirectional, and need to be seen in context. It becomes evident that gene transcription is a balancing act, and the result of various types of modification that are present in the nucleosomes. 2.4. Interplay Between DNA Methylation and Histone PTMs

Although DNA methylation and histone PTMs have been independently presented, both processes are part of the epigenetic network that modulates gene expression. In the literature, it is emerging that they do not act independently, but interact. The two processes may share the same feedback loop model to regulate gene activation or inactivation, as evidenced by factors such as DDM1 (decrease in DNA methylation) jmjC-domain-containing proteins and KYP engaged in both DNA methylation and histone modifications (12). Thus, after DNA replication certain 5-mdC may recruit enzymes and other factors involved in histone modification to establish and maintain the modifications.

3. Tree Development Plant development in forestry species is achieved through a complex genetic network and regulated by multiple environmental and endogenous cues. Dynamic changes between chromatin states facilitating or inhibiting DNA transcription regulate the expression

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of differentiation pathways in response to environmental and developmental signals. The epigenetic code is involved in controlling the functional state of the chromatin and gene expression that underpins the reprogramming of cells necessary for plant development and the survival of species. Efforts made in the field of epigenetics are helping to understand one of the crucial steps during plant ontogenesis that is sexual reproduction. In trees, sexual reproduction starts after a phase change, which allows flowering and seed production in order to ascertain the next generation. The genome-wide distribution of epigenetic marks, known as “epigenome,” has been the subject of extensive studies in recent years, and the “methylome” of Arabidopsis was recently presented (11). Although most studies related to epigenetics are carried out in Arabidopsis, epigenetics in trees is of great interest since these life forms are long-lived and many tree species involve a breeding program for reasons of economic interest. There is a lack of knowledge of sexual reproduction in trees. The contribution of epigenetic dynamics during flowering, fertilization and embryo development is dawning, with prospects of developing deeper insights. In trees, the most widely studied epigenetic mark is DNA methylation, playing a role in many physiological topics such as flowering (18), somatic embryogenesis (19), and active growth (20). These processes appear to concur with changes in DNA methylation and/or histone modifications. DNA demethylation is required prior to entering any of these development programs. This variation in DNA methylation and histone modifications associated with development status is known as epigenetic plasticity. Throughout ontogeny, every developmental stage has its characteristic DNA methylation pattern. When this pattern is not followed, aberrant behaviors appear (21). 3.1. Flowering

The molecular aspects of floral initiation are best understood for herbaceous species. Therefore, a brief overview of the control of floral initiation of Arabidopsis precedes the discussion of trees and woody plants. Floral initiation includes all development steps necessary for the irreversible commitment by the meristem to produce an inflorescence. Epigenetic reprogramming modifying gene expression was demonstrated during floral transition similar to that defined in other developmental processes in plants and in mammals. The transition from the vegetative to the reproductive phase is arguably the most dramatic development change in the plant’s life cycle. The regulation of this important process is achieved by a complex genetic network that monitors the developmental state of the plant as well as environmental conditions such as light and temperature (22, 23). Genetic analysis of flowering-time mutants in Arabidopsis has allowed the identification of 80 genes placed in multiple genetic pathways that control floral transition (24). The integration of environmental and developmental parameters

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is decisive for reproductive success in plants, and in several studies a relation with epigenetic mechanisms such as DNA methylation and histone modification was demonstrated (25, 26). Transitions between different developmental phases in the shoot apical meristem involve changes in the pattern of cellular differentiation and organ formation. Meristem cells are organized at different levels, and the central cells remain pluripotent, while cells in the periphery contribute to organ formation and eventually differentiate (27, 28). This zonation is established during vegetative development of the plant; however, DNA replication patterns are extensively altered during floral transition and concurrent reprogramming takes places (22). The cells of the central zone start to divide at a high frequency and the zonation is lost (18). These changes in apical meristem are genetically and epigenetically regulated (18, 29–31). It has become apparent that epigenetic control of transcription is mediated through specific states of chromatin structure (32). Associations of DNA methylation, histone modifications, and specific chromosomal proteins are involved in controlling chromatin states (17, 32, 33). Epigenetic control plays an essential role in the process of cellular differentiation, allowing cells to be reprogrammed in order to generate new differentiation pathway (3, 31, 34). The regulation of the FLOWERING LOCUS C (FLC) gene in Arabidopsis provides a plant model of how chromatin-modifying systems have emerged as important components in the control of transition to flowering. Genetic and molecular studies have revealed three systems of FLC regulation: vernalization, the autonomous pathway, and FRIGIDA (FRI). All these involve changes in the state of FLC chromatin by DNA methylation and/or histone modification (26, 31, 35, 36). There is growing evidence that chromatin remodeling is involved in numerous processes of development and differentiation in plants (17, 37, 38). DNA methylation and histone modification have been revealed as hallmarks that establish the functional status of chromatin domains (39) and confer the flexibility of transcriptional regulation necessary for plant development and adaptive responses to the environment (4, 40, 41). The results in shrubs (woody plants) indicate that epigenetic mechanisms such as DNA methylation and histone H4 acetylation have opposite and particular dynamics in the apical shoots meristem during the transition from vegetative to reproductive development (42). Global levels of DNA methylation and histone H4 acetylation as well as immunodetection of 5-mdC and acetylated H4, in addition to a morphological study have permitted the delimitation of four basic phases in the development of the Rhododendron sp. bud and allowed the identification of a stage of epigenetic reprogramming which showed a sharp decrease of whole DNA methylation (43) similar to that defined in gametogenesis and embryogenic preimplantation in mammals (2). This epigenetic

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reprogramming is likely to be needed for totipotency, correct initiation of gene expression during floral transition, and early floral development. The epigenetic control and reorganization of chromatin seem to be decisive for coordinating floral development in Rhododendron sp. DNA methylation and H4 deacetylation act simultaneously and coordinately, restructuring the chromatin and regulating the gene expression during shoot apical meristem development and floral differentiation in woody plants. 3.2. Sexual Embryogenesis

In mammals it is well known that epigenetic marks during gametogenesis and early embryo development are erased, and then reestablished according with cell fate (44). Similar to mammals, plants undergo genome-wide demethylation during female gametogenesis leading to the reprogramming needed to control embryogenesis. During Arabidopsis sexual reproduction, it has been demonstrated that DNA methylation levels decreased not only in the female gamete (45) but also in the male gamete (46) prior to fertilization. It has been proposed that loss of methylation in the female gamete is due to the dilution of MET1 (METHYLTRANSFERASE1) during cell divisions prior to fertilization (45). Afterward, when fertilization takes place and new developmental patterns are imposed, methylation is reestablished. In chestnut (Castanea sativa), recent studies into sexual reproduction have shown that subsequent to fertilization, a transient global DNA demethylation is necessary in order to establish the sexual embryogenic pathway (47). This paper is the first to describe the role of DNA methylation in sexual reproduction in a woody species. Furthermore, it was shown that during sexual embryo development, cotyledons maintain constant DNA methylation levels while the embryonic axis shows an increase in DNA methylation until seed maturity is reached. Similar results were obtained for Silene latifolia studying the immunolocalization of 5-mdC during embryo development (18). When the proper pattern is not followed, abnormal plane and cell division during early embryogenesis is observed resulting in reduced viability in mature seeds (48). Loss of function of methyltransferases such as MET1 and CMT3 (CHROMOMETHYLASE3) can mediate the same effects, with purportedly a change in gene expression related to embryo development. The epigenetic machinery in plants provides a fast response time to external factors. This allows cells to adapt to the biotic or abiotic signals rapidly. DNA methylation is known to play a role in silencing of transgenes, as a protection strategy (49). The phenotypic plasticity of plants could not perform without an efficient and accurate mechanism of gene activation–repression. Part of the DNA methylation marks accumulated in plants throughout development can be transferred to the offspring taking into account that germ lines are formed from somatic cells. Thus, there are evidences of epigenetic memory, defined as “transgenerational inheritance

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of epigenetic states” (45). Nevertheless, it is not possible to accumulate epigenetic marks in every generation, which would be incompatible with embryonic development where totipotency of cells is required in order to give rise to valid embryos. However, some steps during gametogenesis and early embryogenesis require expression of genes from one of the parents or a specific ratio of expression, as is the case with endosperm. Epigenetic modifications play a seminal role in this specific control of gene expression. Moreover, transgenerational inheritance of information contained in the epigenome of an individual germ line must go through meiosis and postmeiotic mitosis in order to form the gametophyte, fertilization, embryogenesis and vegetative development of the new generation until the start of a new cycle (50). The accumulation of epigenetic marks and its transgenerational transmission has been suggested to be considered as non-Mendelian inheritance (40), constituting a rapid way of adaptative evolution (51). Methylation of CG is necessary in order to maintain the epigenome stability. When using mutants for conserving CG methylation, the functionality of other epigenetic mechanisms were lost and aberrant phenotypes presented through generations (37). Imprinting is defined as the “epigenetic modification of maternally and paternally inherited alleles that leads to their differential expression in a parent-of-origin-dependent manner” (52). DNA methylation is, then, an efficient mechanism to control gene expression. This phenomenon was first described in maize (53) and afterward in mammals (54). Evolution of imprinting mechanisms in plants and animals has followed different ways, but converge to control crucial steps of sexual reproduction (55). In contrast to mammals, which reset imprinted genes during gametogenesis, plants maintain the epigenetic status. The default mammal status of imprinted genes is active, while in plants it is repressed (56).This main difference between animals and plants may be due to the tissue fate. While mammal tissues are conserved most of the times in the individual, there are parts of the seed that have a transient function during the ontogenesis. The endosperm, the most studied tissue in which imprinting acts, contains a maternal copy of the FWA gene that permanently lost methylation through site-specific DNA glycosylation (57). Since the tissue is destined to die after germination of dicotyledonous species, DNA methylation does not need to be reinstated or maintained. There are many genes involved in plant sexual embryo development (58). Of the genes related with embryo development, the genes controlling this process epigenetically are predominantly DEMETER (a DNA glycosylase gene), MET1, CMT3, DOMAINS REARRANGED METHYLASE1 (DRM1), and DRM2. The interaction between the products of these genes will determine partially the correct expression of the imprinted genes (59). Imprinting is strongly involved in sexual reproduction, specifically

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after fertilization in the first steps of the embryo formation when the development pattern is established. Moreover, it is required for the correct formation of the endosperm, which constitutes in many types of seeds a source of energy for the embryo. 3.3. Somatic Embryogenesis

Somatic embryogenesis is the process by which somatic cells develop into plants through characteristic morphological stages that resemble zygotic embryo development. This is an alternative propagation technique to traditional procedures, presenting numerous applications in plant breeding (60). Moreover, production of embryos under in vitro conditions is a key experimental system to study cell division and reactivation, morphogenic competence, or rejuvenation (61). Since the first reports on somatic embryo formation (62, 63), somatic embryogenesis cultures have been successfully achieved for many angiosperms and gymnosperms species (64–69). Embryogenic cultures can be obtained either from explants cells that are already preembryogenically determined (70) or from somatic cells previously dedifferentiated by using stressful conditions such as nonoptimal salt concentration (71), or plant growth regulators (PGRs) such as auxins, of which 2,4-dichlorophenoxyacetic acid (2,4-D) is most widely used. The induction of somatic embryogenesis entails the end of a current gene expression pattern in the explants tissue, and its replacement with an embryogenic gene expression program (72). Cell differentiation and development are controlled by temporal and spatial activation and silencing of specific genes. Epigenetic changes are a possible mechanism for regulation of current gene expression. During somatic embryogenesis, DNA methylation levels are essential for the acquisition of embryogenic competence and subsequent proliferation and morphogenesis (73–76). Moreover, the treatment of the somatic cultures with 5-azacytidine, a demethylating drug, caused a loss of regeneration capacity in embryogenic lines by arresting the production of somatic embryos (77). A relationship between the embryogenic potential of somatic cultures and DNA methylation levels has been also established. DNA hypermethylation levels have been reported in nonembryogenic callus of Eleutherococcus senticosus compared with embryogenic callus (78) and in Dactylis glomerata significant differences in DNA methylation were observed in embryogenic and nonembryogenic calli from the same genotype, cultured under identical conditions (74). In Pinus nigra Arn. cell cultures, lower methylation levels were found in the line considered as effectively embryogenic (79). Changes in the methylation pattern observed during development and maintenance of embryogenic cultures show that DNA methylation may be involved in the regulation of the embryogenic program genes at the level of chromatin remodeling under the control of PGRs (80).

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3.4. Aging and Maturation

DNA methylation is essential for normal functioning and identity of most somatic cells along lifetime of plants. Recent work demonstrates that loss of both CG and non-CG methylation can render plants unviable in a single generation (46). Multiple abnormalities were observed in methylation mutants from the earliest stages of embryogenesis through reproduction. This makes the hypothesis that DNA methylation is required for proper plant development attractive. An alternative explanation is that severe reductions in DNA methylation alter chromosome stability and function (81). DNA methylation is maintained by DNMTs during development but the epigenome is dynamic, as it exhibits changes during the aging process. When the first mutants for DNMTs were available the mainstream hypothesis was that DNA methylation selectively shuts down genes whose expression is no longer required as the plant transitions through the vegetative, flowering, and reproductive phases of the life cycle (82). However, this idea has not been investigated in greater depth, and evidence for changes in DNA methylation associated with regulation of a gene’s expression is limited. Some studies have compared global DNA methylation levels in plant tissues and observed subtle differences, supporting this hypothesis. In general, animals have their major epigenetic switches during early developmental stages. Plant cells still have the potency to undergo major changes at later stages, including not only transition from vegetative to floral organs but also root formation from stem and leaves or shoot formation from differentiated organs (83). Maturational changes are particularly persistent and difficult to reverse in conifers, as has been demonstrated in several species (84). Differences in the extent of DNA methylation were found between meristematic areas of juvenile and mature Pinus radiata D. Don. trees, whereas differences between differentiated tissues were small (85, 86). Another species of interest is C. sativa, of which both the juvenile and mature phases may occur on the same mature tree. The upper parts of a tree exhibiting determinate growth are chronologically younger and often exhibit mature characteristics, whereas the lower, physiologically older parts may retain juvenile attributes. In this system, ontogenic development involves an increase of global DNA methylation in shoot apex during active growth, but the differences are reset with induction of dormancy (87). The observed changes in extent of DNA methylation during aging and reinvigoration indicate that this form of epigenetic modification modifies the physiological response, with aging and reinvigoration at opposite ends of the scale. Increases in global DNA methylation of vegetative tissues appear incompatible with the activation of some specific genes needed for the reproductive transition in reproductive tissues. However, in chestnut and azalea flowers the differentiation period converges with a mild and temporal decrease of genomic DNA methylation (42, 87).

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Global DNA methylation levels are specific for age, species, tissue, and organ in both plants and animals. In the former, the age-dependent demethylation of DNA is evident, and some investigators consider the degree of DNA methylation as a measure of the biological clock that assesses age and forecasts life span. Distortions in DNA methylation may lead to premature aging (7, 88, 89). Until recently, little was known about global DNA methylation with respect to aging and development in plants and information was not conclusive (21, 39, 90–93). Using a method developed for HPCE (85, 94) a gradual increase in global DNA methylation associated with aging was established for several forest tree species (3). By HPLC analysis, immature tomato tissues such as stems, leaves, and roots were showed to be less methylated than mature leaves, fruits, or seeds (95). In animals aging involves, among other processes, site-specific epigenetic changes such as promoter hypermethylation of CpG islands, associated with gene silencing; and DNA hypomethylation of CpGs dispersed throughout repetitive sequences as well as of some transcriptionally relevant regions. DNA hypomethylation promotes genomic instability, amplification of oncogenes, and also silencing of the genes through an RNAi mechanism (96). Recent analysis of whole genome using Illumina’s GoldenGate methylation platform in human tissue samples showed that loci within CpG islands became more methylated with age, but outside these CpG islands methylation decreased with age (97). Despite the well-known differences between animals and plants, certain similarities such as oxidative stress damage and telomere shortening are present among organisms. Aging studies related to global DNA methylation in plants are not available yet and the knowledge about epigenetic events concomitant with plants aging is in its infancy, possibly because of a more complex development. While the outcome of animal embryogenesis is that all organs are initiated and/or developed, plant embryogenesis results only in a bipolar structure: most organs of the mature plant are formed postembryonically. These distinctive developmental strategies of plants and animals concur with different tasks of their stem cells. Whereas the major task of an animal stem cell is to replenish highly specialized body cells with a limited life span, the plant’s corresponding meristematic cells provide the material for the continued formation of new organs or in some cases new organisms (98). AFLP analysis using methylation-sensitive restriction enzymes identified differentially digested fragments among Arabidopsis cotyledons, leaves, and flowers (29) and between rice seedlings and adult plants (99). While the significance of these experiments is unclear, they indicate that whole genome methylation profiling is a viable concept, at least for the sequenced genomes, with the potential to identify the sequences that are subject to DNA methylation with aging. Two recent studies have profiled the DNA methylation

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pattern of the Arabidopsis genome by immunoprecipitating DNA from adult plants with a 5-methylcytosine antibody and hybridizing it to tiling arrays that cover the entire genome (11, 100). Both groups observed high methylation in areas with the highest density of repetitive elements. They also found that approximately one third of genes contain patches of DNA methylation within their transcribed regions, with far fewer genes being subject to DNA methylation in their promoter regions. The distribution of DNA methylation within transposons and genes is distinct; transposons are heavily methylated along the entire length, whereas within genes DNA methylation is present more prominently in 5¢ regions. 3.5. Dormancy

The phenological event that best describes the seasonal adaptation capacity in perennial plants is bud dormancy. Bud formation and growth cessation are the main phenological variables in the characterization of ecological adaptability, distribution and reproductive success (101). Trees are among the perennials that are strictly bound by these events, since early resumption or late cessation of growth may have severe consequences for these long-lived growth forms. The structures of buds and seeds are designed to overcome environmental conditions that are not suitable for plant growth. These resting organs need to cope with harsh temperatures and restricted water availability for prolonged periods of time, which imposes stress. To handle these difficult conditions, both buds and seeds have developed the ability for dormancy. Although primarily a block to subsequent growth, the function of dormancy is to spread growth across time but in synchrony with the seasons. This makes dormancy an important trait with benefits for survival. Bud dormancy imposition and release are two complex and gradual processes that are induced, imposed, and maintained by exogenous and endogenous factors such as temperature, nutritional state, photoperiod, phytohormones, phytochromes, and others (102). Important inducing factors during dormancy imposition are hormonal and environmental signals, which exert their effect through activation/inactivation of gene expression programs that dictate para-, eco-, and/or endodormancy (103). The presence of 5-mdC in the promoter regions and coding sequences of specific genes alters the binding of transcription factors and other proteins to DNA (104, 105), thereby impeding transcription and causing gene silencing (106). The highly conserved histone proteins at the heart of the chromatin structure (H3, H4, H2A, H2B, and H1) function as building blocks to package eukaryotic DNA into repeated nucleosomal units, folded into higher-order chromatin. Acetylation of core histone tails, among other forms of posttranslational modification, plays a fundamental role in transcription regulation. Evidence of links between DNA methylation and histone hypoacetylation is accumulating (107). Several proteins that

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specifically bind to methylated DNA are associated with complexes that include HDACs. In addition, DNA methyltransferases appear to interact with HDACs (108). In Arabidopsis the WD40 repeat protein HOS15 confers cold tolerance which involves deacetylation of histone H4 and thus inactivation of transcription of downstream genes such as RD29A (109). Cold tolerance is acquired by C. sativa trees at the end of the growing season when temperatures drop, and when buds develop and dormancy is induced. There is growing evidence that chromatin remodeling is involved in dormancy progression (110–113). Acetylated H4 increases and methylated DNA decreases during dormancy break in potato tubers (114). A relationship between global DNA cytosine methylation, acetylated H4 histone, and bud dormancy in C. sativa was demonstrated (115). Increased methylation levels in the terminal buds coincided with bud set, while decreased methylation levels coincided with bud burst. Intermediate buds with paradormancy were characterized by reduced fluctuation in DNA methylation, particularly during bud burst. Furthermore, using immunodetection, acetylated histone H4 levels from terminal buds were found to be higher during bud burst than during bud set. Thus, global DNA methylation and acetylated histone H4 levels showed opposite patterns and coincided with changes in bud dormancy in C. sativa. Not surprisingly, differences in transcription were observed, allegedly as a result of these epigenetic changes. The dormancy transcriptome of C. sativa apical buds characterized by generating forward and reverse cDNA subtraction libraries, revealed association of nondormancy with genes in the functional groups for energy; protein with binding function or cofactor requirement; protein synthesis; biogenesis of cellular components; cell cycle and DNA processing. On the other hand, dormancy was associated with stress-related genes; and genes for cell rescue, defense and virulence; interaction with the environment; systemic interaction with the environment. A transcriptome comparison of bud dormancy in C. sativa and published data for seed dormancy in Arabidopsis demonstrated a core set of genes that are likely to play a principal role (116). These included stress-associated genes and one gene conferring an epigenetic mark (117). A general role for epigenetics in dormancy seems to emerge.

4. Plant Cell Reprogramming In plants, regeneration of new organs from somatic cells has been known for a long time, but the mechanisms focused to dedifferentiate somatic cells, which are already differentiated, and change their fate enabling the formation of roots, shoots and damage repair are not fully known (118).

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Cellular reprogramming involves a rewiring of epigenetic and transcriptional parameters (119). Reprogramming can be induced by molecularly undefined means, using an environment of components or elements that are largely unknown to achieve cellular reprogramming. An example would be fusion of somatic cells or somatic cell nuclear transfer, with unknown factors present in the cytoplasm involved in reprogramming of the nuclei (120). In contrast, direct reprogramming methods use defined genetic or nongenetic elements to induce reprogramming of the cell. Transcription factors and specific culture media with known components such as growth regulators are responsible for this reprogramming (121, 122). In organ formation of both adventitious and regenerated organs in Arabidopsis, a reversion to stem cell niche activity is not necessary for in vivo early-root tip regeneration from developmentally young cells (123). However, the formation of a stem cell niche from competent callus cells obtained from young seedlings during in vitro plant organogenesis (118). Redifferentiation efficiency is much higher in tissues at earlier stages of development (86). Even callus cells from adult tissues show a lower proliferation rate and lower regeneration capacity than those induced from juvenile tissues (124). 4.1. Redetermination

Many pathways and strategies are possible from early to later stages of regeneration in both animals and plants depending on the progenitor cells (125). Despite the diverse regeneration mechanisms, most phenomena in one kingdom seem to have a counterpart in the other. Therefore, another interesting point would be to understand the mechanisms of redetermination of fully differentiated progenitor cells that do not pass through a callus state to regenerate (direct organogenesis), especially in relation to the developmental age of cells and tissues. Propagation of plants through tissue culture can induce a variety of physiological, genetic, and epigenetic changes.

4.2. Molecular Aspects of Reprogramming

In plants, cell plasticity enables somatic cells to begin new developmental programs generating adventitious organ formation in the presence of the appropriate plant growth regulator. Somatic embryogenesis and adventitious shoot formation are practical examples of cell reprogramming (124, 126). Morphogenesis and adventitious organogenesis are complex processes of cell plasticity, and according to Christianson and Warnick (127), they can be divided in three stages: acquisition of competence, induction, and morphological differentiation. In adventitious caulogenesis, somatic cells respond to the hormonal stimulus with a reprogramming process achieving a new cell fate. Cytokinins are the most efficient plant growth regulators in the induction of this process. In Arabidopsis, histidine protein kinases are cytokinin receptors,

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and histidine phosphotransferases transmit the signal to response regulator in the nucleus activating or repressing transcription (122). Some genes have been already described to be related to the adventitious bud formation process. Examples are cytokinin response 1 (CRE1) (128) taking part in the cytokinin hormone receptor; enhancer of shoot regeneration 1 (ESR1) allowing the development of cytokinin independent shoots (129); the gene family NO APICAL MERISTEM (NAM); CUP SHAPE COTYLEDON genes (CUC1 and CUC2) that have an additional function related to cotyledon separation (130–132); and PkMADS1 (133) for which expression is only observed in the apex and in tissues producing adventitious shoots. Global programs of gene expression during shoot and root development involved in cytokinin and auxin signaling have been revealed by microarray hybridization demonstrating the effects of gene families and their interaction (134, 135). Regarding somatic embryogenesis several biological studies show a different effect of growth regulators during the process (19, 60), and different gene families such as LEAFY COTYLEDON (LEC) or AGAMOUS-LIKE (AGL) are overexpressed, while ectopic expression is sufficient to promote somatic embryogenesis (136). 4.3. Genetic Stability of Clones

Somaclonal variation is the genetic variation that is observed when plants are regenerated from cultured somatic cells, and was first detected by the high frequency of qualitatively segregating phenotypes observed among progeny of plants that were expected to be genetically identical (137). It has been used to generate desirable traits, but the results have not met the expectations (138). This genetic variation is heritable and usually reduces the commercial value of micropropagation of valuable elite clones, which is a problem in breeding and propagation techniques that involves adventitious regeneration. Various types of mutations have been described in somaclonal variants including point mutations, gene duplication, chromosomal rearrangements, and chromosome number changes (139). Somaclonal variation takes place in plants generated via adventitious shoot or somatic embryo formation, in particular after an intermediate callus phase (140, 141). Micropropagation and somatic embryogenesis, via suspension cultures, may also suffer from somaclonal variation (142). A number of different molecular techniques are currently available to detect sequence variation between closely related genomes such as those between source plants and somaclones. Main techniques include random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs) (87, 143, 144). Both techniques are useful in comparing the DNA from any number of different samples for the differentiation of plants because of sequence variation by identifying random polymorphisms. There are also some approaches to measure somaclonal variation by statistical analysis for in vitro culture (145).

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4.4. Epigenetic Stability of Clones

5. Tissue CultureInduced Phenotypic Variations and DNA Methylation

Genetic alterations can cause epigenetic changes which are not hereditary and which confer stable phenotypes and persist even in the absence of an agent or inductive condition. These epigenetic changes are caused by alterations in DNA methylation, in histones, or through other epigenetic modifications. Usually, these modifications last until the effect of the of the inducing condition disappears (146), but there are several reports stating that these changes may be transferred by sexual propagation and even have the capability to persist during in vitro culture (147, 148). In a similar way, especially in forestry species, a prior modification of the DNA methylation levels sometimes allows increased success in the in vitro culture. This situation happens in a reinvigoration process where a decrease in DNA methylation takes place (85). It has been suggested that changes in the epigenetic status of a plant tissue cultured in vitro could be caused by an incomplete resetting of the epigenetic marks, but stress is also known to provoke epigenetic changes such as transposon activation and activation or deactivation of the methylation status of loci (16, 149, 150). Even using different plant growth regulators showed big genetic differences and one might wonder if the differences in methylation in plants cultured in vitro is the result of culturing or of additional processes such as wounding, asepsis, or hormone application.

One of the molecular mechanisms responsible for in vitro cultureassociated phenotypic changes is DNA methylation which generates somaclonal variation by an indirect pathway; that is, without involvement of genetic changes. Low levels of DNA methylation are known to affect normal plant development (21), and have an effect on the gene–environment interaction (151). Furthermore, variation in DNA methylation of specific genes causes different patterns of flower symmetry (152). The effects of somaclonal variation are detectable in various phenotypic traits, from bushiness in the ornamental crop Zantedeschia to leaf shape in begonia. The most studied species with aberrant development as a result of somaclonal variation is the crop Elaeis guineensis, because of its economic importance. Oil palm in vitro propagated may show aberrant flowers, also known as mantled, because they develop a second whorl of carpels instead of stamens (153). Most of the genes found related to this change are members of the MADS box transcription factor family. (154) have found epigenetically regulated genes related to auxin response, although no direct correlation was found for mantled flowers and methylation of specific genes. A similar issue was observed in cauliflower, but this seemed to be more related to nuclear DNA content rather than to DNA methylation (155).

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Results obtained with MADS box genes and with genes related to hormone response have an important effect in somaclonal variation because of the role played by cytokinins (156), encouraging scientists to study epigenetic mechanisms that might explain the observed changes.

6. Conclusions DNA methylation is implicated in the correct transition between stages of plant development (i.e., flowering, dormancy, etc.). Plants have common and distinct DNA methylation mechanisms compared with animals, summarized in three different classes of DNA methyltransferases: the MET1 family, which acts as the homologue to the mammalian DNMT1 family; the chromomethylase family, which preferentially methylates CpNpG sequences; and de novo methyltransferases, which are homologous to the mammalian DNMT3 family. DNA methylation is stable during development, albeit not static, and contributes to cellular plasticity. Cellular differentiation is associated with an initial DNA demethylation, which permits later cellular reprogramming. Specific DNA demethylation is related to flowering, stem cell differentiation, etc. The formation of germ-line cells late in development allows the transmission of stable epigenetic information acquired during the life cycle. This involves several different epigenetic mechanisms including DNA methylation, histone modifications, and siRNA.

Acknowledgments Scientific progress in aging, phase change, reinvigoration, and markers for quality was made with financial support from EU Projects FAIR3-CT96-1445, INCO 10063, and MCTAGL2000-2126, AGL 2004-00810/FOR, AGL2007-62907/ FOR Spanish National Projects. The Spanish M.E.C.D. supported fellowships of all young researchers. References 1. Surani MA, Durcova-Hills G, Hajkova P et al (2008) Germ line, stem cells, and epigenetic reprogramming. CSH Symp Quant Biol 73:9–15 2. Morgan HD, Santos F, Green K et al (2005) Epigenetic reprogramming in mammals. Hum Mol Genet 14:47–58 3. Valledor L, Hasbún R, Meijón M et al (2007) Involvement of DNA methylation in tree

development and micropropagation. Plant Cell Tissue Organ Cult 91:75–86 4. Grant-Downton RT, Dickinson HG (2005) Epigenetic and its implications for plant biology 1. The epigenetic network in plants. Ann Bot 96:1143–1164 5. Lanzuolo C, Orlando V (2007) The function of the epigenome in cell reprogramming. Cell Mol Life Sci 64:1043–1062

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Chapter 23 The Potential Roles of microRNAs in Molecular Breeding Qing Liu and Yue-Qin Chen Abstract microRNAs (miRNAs), a class of small, endogenous, noncoding RNAs, are uncovered to play greatly expanded roles in a variety of plant developmental processes by gene silencing through inhibiting translation or promoting the degradation of target mRNAs. In virtue of their ability to inactivate either specific genes or entire gene families, artificial miRNAs function as dominant suppressors of gene activity when brought into a plant. Moreover, artificial target mimics are applied for the reduction of specific miRNA activity. Consequently, miRNA-based manipulations have emerged as promising new approaches for the improvement of crop plants. This action includes the development of breeding strategies and the genetic modification of agronomic traits. Herein, we describe the current miRNA-based plant engineering approaches, and their advantages and challenges are also stated. Key words: microRNA, Molecular breeding

1. Introduction Due to an increasing world population, as well as scarcity of arable lands and water, global climate changes, and the demands for biofuels as substitutive energy sources, sufficient future global production of food from crop plants is of serious concern (1). To overcome these problems, new agricultural technologies will be needed to ensure global food supply and security, with no regard to the efforts of conserving water and lands (2). Plant molecular breeding seems to be an efficient and economic means of tailoring crops to improve their qualitative and quantitative traits including tolerance to biotic and abiotic stresses. The rapid advance in knowledge on genomics and proteomics will certainly be beneficial to fine-tune the molecular breeding approaches so as to achieve a significant progress in crop improvement in the near future.

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_23, © Springer Science+Business Media, LLC 2012

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Recent studies have begun to reveal powerful and unexpected roles for microRNAs (miRNAs) in controlling plant growth by native gene silencing. miRNAs have been reported to modulate various aspects of plant development, including leaf morphogenesis and polarity, root initiation and development, floral differentiation and development, vascular development and transition of plant growth from vegetative growth to reproductive growth (3, 4). Moreover, miRNAs are also involved in phytohormone signal transduction (5) and signal transduction in response to environmental stress and pathogen invasion (6, 7). These regulatory miRNAs stimulate the idea of developing artificial miRNAs to silence specific gene(s), allowing for the direct molecular modulation of plant traits, which can be applied to crop species for breeding. Additionally, another layer of modulation in miRNA action has been reported by Franco-Zorrilla and his colleagues when studying phosphate starvation (8). The IPS1 sequence which encodes a noncoding RNA, contains a three-nucleotide insertion in the motif that is highly complementary to the sequence of miR399. This characteristic prevents the normal cleavage of IPS1 and thus sequesters the action of miR399. Based on these features, artificial target mimics were born to exceptionally reduce the miRNA activity (9). This method can be applied to study the function of miRNA and reversely modulate agronomically related miRNAs to facilitate molecular breeding. Here, we summarize the already known miRNA-based approaches in plant engineering and lastly consider the modulation feasibility and future challenges for putting these approaches into practical use in breeding program to increase crop yield.

2. miRNAs Modulation as an Innovative Approach to Plant Engineering

Some lessons learned from existing antisense technology and gene engineering approaches can be adapted to manipulate specific genes or miRNAs levels in vivo (Fig. 1). To date, there are two methods available to selectively target miRNA pathways. Presently, short-hairpin RNAs based on miRNA precursor backbones (artificial miRNAs (amiRNAs)) are the most successful expression cassettes to induce highly specific gene silencing in plants (10). Expression of amiRNA precursors can generate mature amiRNAs with high specificity similar to natural miRNAs to cleave their target genes (11) (Fig. 1b). Moreover, target mimics, consisting of a noncleavable RNA that forms a nonproductive interaction with a complementary miRNA, provide a new policy that can be used to inhibit the activity of specific miRNAs (8, 9) (Fig. 1c).

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Fig. 1. miRNA-based technologies to regulate gene expression in vivo in plants. (a) Following transcription, the pri-miRNA is processed by DCL1, perhaps with the aid of HYL1 and other factors, to a miRNA:miRNA∗ duplex. The mature miRNA is incorporated into a silencing complex that includes AGO1 which then mediated the degradation of mRNA or its translational repression. (b) AmiRNA is engineered into a miRNA precursor using overlap PCR to replace the endogenous miRNA sequence. The pri-amiRNA is processed by DCL1 and function as normal miRNA. (c) Artificial target mimic is a noncleavable RNA which is not cleaved but instead sequesters a complementary miRNA. The perfect sequence complementarity allows the target mimic to bind to the miRNA and interfere with miRNA function.

2.1. Artificial miRNAs

RNA silencing is a natural regulatory mechanism of eukaryotes modulating endogenous gene expression. Generally, doublestranded RNAs (dsRNAs) or hairpin RNAs (hpRNAs) are processed into small interfering RNA (siRNA) or microRNA (miRNA) duplexes by specific enzymes (12). Then these small RNAs are incorporated into the RNA-induced silencing complex (RISC) to guide the degradation or translation repression of mRNA targets. Thus, miRNAs and siRNAs can affect gene expression in animals and plants by posttranscriptional gene silencing. Recently, more and more reports have demonstrated that the alteration of several nucleotides within the miRNA sequence does not affect its biogenesis and the positions of matches and mismatches within the precursor stem loop remain unaffected. Because of these features, artificial miRNAs can be created by exchanging the miRNA/miRNA* sequence within miRNA precursor genes. Furthermore, the genome-wide gene expression analyses have also demonstrated that plant amiRNAs have similarly high specificity as endogenous miRNAs. Thus, miRNA sequences can easily be optimized to knock down a single gene or highly conserved gene families without affecting the expression of other genes (11, 13). Based on these results, for gene engineering to improve agronomical traits, amiRNAs can be designed to target any gene in need with great specificity. AmiRNAs share many properties with siRNAs. However, differences still exist. Particularly, a diverse set of siRNAs can be produced from the complete dsRNA; thus, siRNAs not only target

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candidate RNAs but also can affect RNAs that are not perfectly complementary, generally considered off-targets, while an amiRNA precursor gives rise to only a single small RNA species without extensive homology to any plant genes that can be optimized to avoid off-target effects (10, 13). Besides, it has been reported that transgene-derived or viral-induced siRNAs are able to move from cell to cell, indicating that their functions are nonautonomous, whereas miRNAs are not mobile and act cell autonomously (13, 14). Finally, amiRNA-mediated method has no environmental biosafety problem when applied in agriculture (10). In summarize, these predominances make the application of amiRNAs credible for plant molecular engineering to a large extent. Nowadays, the amiRNA-based gene silencing technique has been used successful as expression cassettes to induce highly specific gene silencing not only in higher plants (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Lycopersicum esculentum, and Nicotiana tabacum) but also in lower plants (Physcomitrella patens), as well as unicellular organisms (Chlamydomonas) (10, 11, 13, 15–18). The results showed that custom-made, synthetic miRNAs vectored by endogenous pre-miRNA backbones produced phenocopies of multiple mutant combinations of genes that are not naturally regulated by miRNA, suggesting the feasibility that amiRNAs can be used successfully to target any candidate genes other than the one which are natural targets of endogenous miRNAs (2). As a model plant for monocots, rice is also one of the most important staple crops in the world (16). Fortunately, the successful use of amiRNAs for the specific downregulation of genes was also shown for rice. This action has been utilized effectively to improve the significant agronomic traits and at last increases the crop yields (16). Besides, the successful application of amiRNAs to mediate specific gene silencing was demonstrated not only in indica rice but also in japonica rice. Most importantly is that the transgenes are stably inherited and they remain effective in the progeny. This remarkable characteristic paves a way for amiRNAs-based gene silencing to regulate agronomically important traits in varieties used in modern breeding, with the ultimate intention of improvement of agronomic performance and nutritional value (2, 16). Lastly, since rice shares excellent gene colinearity with other monocots such as wheat and maize, amiRNAs-mediated gene breeding strategy in rice can also be applied to other species to a large extent (16). In the entire life of plant development, plants have to deal with a variety of environmental stresses such as salinity, drought, and pathogen invasion. Generally, RNA silencing in plants is a natural defense system against foreign genetic elements including viruses. Furthermore, it has been reported that short-hairpin RNAs based on miRNA precursors to express the artificial miRNAs (amiRNAs) can specifically target transcripts originally not under miRNA control to induce gene silencing (11, 15). Based on these results, amiRNAs

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appears to be a promising tool for conducting plant virus resistance. So far, the use of amiRNAs in engineering plant virus resistance has been extensively explored. The results declare that the expression of virus-specific artificial miRNAs has been verified to be an effective and credible new approach to engineering plant resistance to CMV (Cucumber mosaic virus) and TuMV (HC-Pro of turnip mosaic virus), and possibly, to other plant viruses as well in the near future (10, 15). To sum up, amiRNA-based approach has been proved to be a highly effective tool to modulate agronomically important traits in different plant varieties used in modern breeding, the ultimate aim of which is to improve the agronomic performance and crop yield (2). With regard to the genes which confer significant agronomic traits and perform as negative regulators, amiRNAs can be engineered to silence these specific genes to satisfy the desirable traits in crop plants. We believe that as long as we expend sufficient effort into this approach, the aim of putting amiRNAs to practice is highly likely to be achieved in plant molecular breeding as soon as possible (2). 2.2. Artificial Target Mimics

In plants, most miRNA targets are cleaved and show much higher complementarity with the miRNAs around the cleavage sites in the coding regions. This characteristic accounts for the generation of target mimicry, which is considered to be composed of a noncleavable RNA which is not cleaved but instead sequesters a complementary miRNA (8). Target mimicry represents an additional layer of regulation in miRNA action by counteractive impact and it was found while studying Pi homeostasis, a critical determinant of growth performance and one process regulated by miR399 (8, 19). IPS1 (INDUCED BY PHOSPHATE STARVATION1) RNAs is involved in response to Pi starvation and contains a region of complementarity with miR399. In comparison to regular miRNA target sites, the IPS1 sequence contains a mismatched loop at the expected miRNA cleavage site, and this bulge in the miRNA–target pair prevents endonucleolytic cleavage of IPS1 transcripts (8). Thus, IPS1 RNA is not cleaved but instead sequesters miR399, leading to a reduction of miR399 activity. More significantly, the IPS1 family members represent an example of natural target mimicry and this mechanism can be exploited to study the effects of inhibiting miRNAs other than miR399 as well as even the entire miRNA families. The nearest report indicated that a large-scale collection of knockdowns for Arabidopsis thaliana miRNA families has been achieved using artificial miRNA target mimics (9). Conceptually, target mimics share much similarity with miRNA sponges which were used to reduce miRNA actions in animals. Both of them are transcripts containing multiple miRNA binding sites that compete with endogenous target mRNAs, thereby reducing the efficiency of the corresponding

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miRNA (9, 20). The difference is that the miRNA cleavage sites of target mimics must be modified to prevent cleavage, but to still allow miRNA binding. Therefore, the plant target mimics used for research are modified from the 23 nucleotides of miR399complementary motif in IPS1 (9). They were designed to knockdown the majority of Arabidopsis thaliana miRNA families. The results showed that one fifth of these transgenic plant lines have obvious morphological defects. Additionally, phenotypes of plants expressing artificial target mimics directed against miRNAs involved in development were in several cases consistent with previous reports on plants expressing miRNA-resistant forms of individual target genes, demonstrating that a limited number of targets mediate most effects of these miRNAs (9). In conclusion, artificial target mimics can be applied successfully to reduce miRNA activity to some extent in plants. According to previous reports, miRNAs have been proved to influence almost every aspect of plant growth and development, with a diverse set directly involved in the modulation of agronomic traits, such as miR164 in lateral root formation and miR165/ miR166 in shoot branching (2). Naturally, miR164 negatively modulate NAC1 mRNA to repress lateral root formation and reduced lateral roots affect the ability of a plant to secure edaphic resources, which ultimately influence crop yields. Engineering target mimics to sequester miR164 is capable for plants to express more lateral roots to sufficiently secure edaphic resources. Similarly, target mimics can also be applied for miR165/miR166 to increase tillers and consequently improve grain yield. As a result, plant artificial target mimics represents a novel technique to modulate endogenous miRNAs levels to improve the agronomic traits in crop plants, with the eventual intention to improve crop output (2).

3. Challenges for Improving the Efficiency of miRNA-Based Approaches

Compared to the conventional targeted gene knockout approaches, though still a relatively new method, the application of amiRNA seems to be at least as effective and versatile as conventional hpRNAi while at the same time promising greater specificity and safety (2, 21). More and more researchers have adopted amiRNA to silencing specific target genes (22). However, limitations are still existed. It is reported that the overall success rate of amiRNA-based gene silencing is close to 75%, suggesting that amiRNAs design is not maximally optimized ( 21, 23 ) . Recent work have indicated that the amiRNA design incorporating perfect complementary to a target gene could be favorable in increasing gene silencing efficiency, and manipulation of amiRNA structure and sequence proves also beneficial to further enhance the

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effectiveness of amiRNA in plants (2, 23). Therefore, progression in the understanding of biogenesis and action of endogenous miRNAs, which appears to be a very active field of scientific inquiry within a long time, should allow further improvement and strengthened sophistication and application of the amiRNA approach (2). From the above indication, we get the knowledge that the application of target mimics to reduce activity for most of the known miRNA families in A. thaliana was proved to be feasible, with 14 out of 71 miRNA families with target mimics led to morphological abnormalities, agreeing with former reports in which miRNAs were overexpressed, miRNA target genes were mutated, or miRNA genes were inactivated by conventional knockouts (9). However, it has to be mentioned that when compared to the conventional gain-of-function or loss-of-function of miRNA mutants, the defects of target mimics transgenic plants were often weaker. For example, plants overexpressing miR172 target mimics displayed absence of altered floral phenotype. One of the reasons may be that many miRNAs affect their targets only in a small set of cells and assaying expression in whole organs would obscure the effects of miRNA downregulation on mRNA levels (9). Moreover, for miRNAs required for embryonic development, only lines with relatively weak expression of the artificial target mimic might have survived. Such defects could be overcome by tissue-specific or inducible expression of target mimics. Nonetheless, though artificial target mimics have limitations, they possess the advantage that they affect all targets simultaneously (8, 9).

4. Concluding Remarks Gene silencing, a powerful genetic tool for knocking down gene expression, is commonly employed to clarify and manipulate biological function of novel, agronomically important genes (23). Plant miRNA, a class of endogenous small RNA, has been demonstrated to play a pivotal role in plant growth and development also by gene silencing using mRNA degradation or mRNA translational inhibition. This station led to the generation of miRNA-based approaches—artificial miRNA and artificial target mimics, used for gene function exploration or modern molecular breeding. The amiRNA technology exploits endogenous miRNA precursors as structural backbones but replacing the stem-loop region with a specific amiRNA sequence, designed to specifically target a selected gene(s) of interest or groups of closely related genes (21). This method could produce amiRNA that have similarly high specificity to naturally endogenous miRNA and guide the RISC to cleave their target genes (11, 21). Thus, the amiRNA sequences can be easily optimized to silence one or several target genes without

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affecting the expression genes (21). Artificial target mimics were generated by the modification of miR399-complementary sites in IPSI to sequester specific miRNA or the entire miRNA families (9). The phenotypes caused by target mimics share extensive similarities with the ones by expressing resistant forms of individual targets, suggesting the feasibility of using target mimics to reduce the activity of miRNA (9). More intriguingly, the researchers also shown that when mimiclike sites are introduced into the 3¢-UTR of a protein-coding gene, they not only are active in sequestering the targeted miRNA but can also reduce protein levels produced by the mRNA linked in cis (9). Since mimic sites are not subject to miRNA slicing, the reduction is thought to occur at the translational level (8, 9). These results give us an intriguing scenario which exhibits that mRNAs containing mimic-like sites, or possibly other sites with reduced complementarity with miRNAs, are regulated by miRNAs exclusively through translational inhibition (9). In conclusion, the miRNA-based approaches could be designed to silence specific genes or miRNAs so as to validate the function of candidate genes, which are responsible for advantageous agronomical traits, and contrarily broaden the usage of these approaches to improve agronomic performance. In a word, amiRNA and artificial target mimics appear as promising methods that are being developed for identifying agronomical trait-relevant genes and putting them to practical use in crop improvement (2). References 1. Brown ME, Funk CC (2008) Climate. Food security under climate change. Science 319: 580–581 2. Liu Q, Chen YQ (2010) A new mechanism in plant engineering: the potential roles of microRNAs in molecular breeding for crop improvement. Biotechnol Adv 28:301–307 3. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Ann Rev Plant Biol 57:19–53 4. Chuck G, Candela H, Hake S (2009) Big impacts by small RNAs in plant development. Curr Opin Plant Biol 12:81–86 5. Liu Q, Chen YQ (2009) Insights into the mechanism of plant development: interactions of miRNAs pathway with phytohormone response. Biochem Biophys Res Commun 384:1–5 6. Chen J, Li WX, Xie DX et al (2004) Viral virulence protein suppresses RNA silencingmediated defense but upregulates the role of

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MicroRNA in host gene expression. Plant Cell 16:1302–1313 Sunkar R, Kapoor A, Zhu JK (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 18:2415 Franco-Zorrilla JM, Valli A, Todesco M et al (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39:1033–1037 Todesco M, Rubio-Somoza I, Paz-Ares J, Weigel D (2010) A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana. PLoS Genet 6:e1001031 Duan CG, Wang CH, Fang RX, Guo HS (2008) Artificial MicroRNAs highly accessible to targets confer efficient virus resistance in plants. J Virol 82:11084–11095

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11. Schwab R, Ossowski S, Riester M et al (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18:1121–1133 12. Qu J, Ye J, Fang R (2007) Artificial microRNAmediated virus resistance in plants. J Virol 81:6690–6699 13. Khraiwesh B, Ossowski S, Weigel D et al (2008) Specific gene silencing by artificial MicroRNAs in Physcomitrella patens: an alternative to targeted gene knockouts. Plant Physiol 148:684–693 14. Tretter EM, Alvarez JP, Eshed Y, Bowman JL (2008) Activity range of Arabidopsis small RNAs derived from different biogenesis pathways. Plant Physiol 147:58–62 15. Niu QW, Lin SS, Reyes JL et al (2007) Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol 25:254 16. Warthmann N, Chen H, Ossowski S et al (2008) Highly specific gene silencing by artificial miRNAs in rice. PLoS One 3:e1829 17. Zhao T, Wang W, Bai X, Qi YJ (2009) Gene silencing by artificial microRNAs in Chlamydomonas. Plant J 58:157–164

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18. Shi R, Yang C, Lu S et al (2010) Specific downregulation of PAL genes by artificial microRNAs in Populus trichocarpa. Planta 232: 1281–1288 19. Fujii H, Chiou TJ, Lin SI et al (2005) A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol 15:2038–2043 20. Ebert MS, NeilsonM JR, Sharp PA (2007) MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4:721–726 21. Ossowski S, Schwab R, Weigel D (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J 53: 674–690 22. Kim J, Somers DE (2010) Rapid assessment of gene function in the circadian clock using artificial microRNA in Arabidopsis thaliana mesophyll protoplasts. Plant Physiol 154: 611–621 23. Park W, Zhai J, Lee JY (2009) Highly efficient gene silencing using perfect complementary artificial miRNA targeting AP1 or heteromeric artificial miRNA targeting AP1 and CA1 genes. Plant Cell Rep 28:469–480

Chapter 24 Determination of Histone Methylation in Mono- and Dicotyledonous Plants Geovanny I. Nic-Can and Clelia De la Peña Abstract Epigenetics includes DNA methylation and histones posttranslational modifications such as methylation, acetylation, phosphorylation among others. One of the most abundant modifications in histone tail is the methylation. It has been found that the methylation pattern in the histone H3 may provide understanding of the process involved in cell differentiation, adaptation, and evolution in plants. In this work, we detail a method for isolation of nuclear proteins from small amount of sample to identify global changes in different lysines of the histone H3 tail by using immunodetection. Key words: Agave fourcroydes, Coffea canephora, Epigenetics, Histone methylation

1. Introduction 1.1. Patterns of Histone H3 Methylation

The nucleosome is the fundamental unit of the chromatin; it is composed of 146 pb of DNA wrapped on a histone octamer which is formed by two copies each of the cores histone proteins H2A, H2B, H3, and H4 (1). The chromatin is a dynamic molecule regulated by multiple epigenetic mechanisms, including DNA methylation, histone modification and by noncoding RNA, which together with the former mechanisms allows the chromatin to relax or to compact creating euchromatin (actively transcribed region) or heterochromatin (transcriptionally silent region), respectively (2, 3). Histone posttranslational modifications (PTMs) play a central role in the epigenetic regulation of gene expression in eukaryotic organisms. These modifications reorganize the chromatin structure in which the DNA is packaged within the cell, controlling cell differentiation and development. Histone PTMs occur mainly on the N-terminal tails of histones. Histone methylation together with

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_24, © Springer Science+Business Media, LLC 2012

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other modifications (acetylation, phosphorylation, ubiquitylation, sumoylation, ADP-ribosylation, deamination, proline isomerization) forms a sophisticated code which is catalyzed by different enzymes at specific amino acids residues (4, 5). Methylation is only found in the lysine (K) residues of the histones H3 (K4, K9, K27, K36, and K79) and H4 (K20), being more abundantly in H3. Lysine methylation can be found as mono, di, or trimethylated, which is controlled by different histone methyltransferases and demethylases (6, 7). Histone lysine methylation is involved in the activation or repression of gene transcription depending on both the position of the lysine that is methylated and the degree of methylation (8). Recent studies in Arabidopsis have shown that trimethylation of histone H3 at K4 is associated with transcribed regions, while di- or trimethylation of histone H3 at K36 is linked to transcription elongation (7, 9). On the other hand, the dimethylation at K9 represses gene expression, and it has been observed that this epigenetic mark is concentrated in heterochromatin regions (10). Another repressor mark of the transcriptional activity well studied is the methylation at K27 in the histone H3. Trimethylation of histone H3 at K27 has been implicated in development regulation to maintain the transcriptional repressed stage of target genes during cell division in Arabidopsis (8, 11, 12). Unlike the dimethylation at K9, the monomethylation of K27 mark is independent of DNA methylation, and it has been observed in heterochromatic regions, whereas di- or trimethylation at K27 is mainly present in euchromatic regions (13). 1.2. Methods for Detection of Histones Posttranslational Modifications

The study of chromatin and epigenetics has grown rapidly in the past few years, and now it has become one of the most outstanding biology areas for plant development research. The genome-wide distribution of the different marks in histones can be determined by mass spectrometry analysis (14), high performance liquid chromatography (HPLC), chromatin immunoprecipitation (ChIP) or ChIP coupled to gene array technology (ChIP-ChIP) (15), and covalent attachment of tags to capture histones and identify turnover (CATCH-IT) (16). Other techniques available are used to examine the distribution of histone variants or histone PMTs, e.g., fluorescent in situ hybridization (FISH) or immunodetection by western blot (2, 17, 18). These and other approaches can be used to understand plant development in response to environmental changes. However, some of them, although they have many molecular advantages, are very expensive to use or require sophisticated software. In the present chapter, we describe a less expensive method to determine histone modifications by western blot which has been modified from current published methods for nuclear proteins (2, 19). This method details the steps used for nuclear proteins extraction from a very small amount of tissue, the transference of nuclear proteins to either a PVDF or a nitrocellulose membrane,

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the incubation protocol of different antibodies to determine the different PTMs in the histone H3 in mono- and dicotyledonous plants, as well as the detection method. 1.3. Analysis of the Epigenetic Changes in Mono- and Dicotyledonous In Vitro Systems

During plant development, transcription regulation is carried out by epigenetic mechanisms (20–22). These epigenetic mechanisms are mainly DNA methylation and histone posttranslational changes that modify the chromatin structure. The histone PTMs are a crucial step to change the structure of chromatin for the reprogram of plant development for acquisition of pluripotency, totipotency or for maintaining the integrity of the genome (23). Recent reports indicated that epigenetic mechanisms are similar in both monoand dicotyledons; for example, in Arabidopsis thaliana the overexpression of SET1 domain proteins decreases in both root and leaf growth, whereas in Oryza sativa it leads to retarded plant growth (24, 25). Furthermore, it has been observed that KRYPTONITE of Arabidopsis and SDG714 of O. sativa, both methyltransferases of the H3K9, play a similar role repressing the expression of transposable elements as Ta3 and Tos17, and in both species the loss of this mark increases gene expression (10, 26). This mechanism of methylation at the H3K9 indicates that the pattern of histone methylation works in the same way to program, establish, maintain, and protect the integrity of the genome in plants.

1.4. Method Advantages

The method presented in this chapter has the advantage of good extraction compared with previous studies (2, 10). This method increases the quantity of protein extracted. By using a small amount of sample, reducing it from 3 g (19) to only 500 mg of tissue, we are able to obtain approximately 200–250 μg of total protein that is sufficient to perform more than 50 blots. Five micrograms of total nuclear protein is enough to transfer to a polyvinylidene fluoride (PVDF) membrane (Immobilon-P) in 3.5 h. The blocking solution used is nonfat milk, and the incubation period with primary and secondary antibodies is 60 and 30 min at room temperature, respectively. The detection method used is chemiluminescence. The method described here for the analysis of histone H3 methylation pattern has been tested with mono- and dicotyledonous species, obtaining reproducible results. The methodology described here is simple, easy, efficient, and reproducible. Furthermore, the membrane can be nitrocellulose or PVDF and be retested with different antibodies to see different marks in the same sample.

2. Materials 2.1. In Vitro Plantlets

The plant material used was embryogenic tissue of the dicotyledonean plant Coffea canephora obtained as described by QuirozFigueroa et al. (27). The monocotyledonean plant Agave fourcroydes

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Fig. 1. (a) Plantlets of Coffea canephora in vitro. (b) Embryogenic system of C. canephora after 2 months of induction. (c) Micropropagation of Agave fourcroydes in vitro. (d) Plantlets of A. fourcroydes obtained in vitro ready to transplant into soil.

was grown at 25 ± 2°C under a 16/8-h (light/darkness) photoperiod (see Fig. 1). 2.2. Histone Isolation

1. Nuclei isolation buffer (NIB): 15 mM PIPES pH 6.8, 5 mM MgCl2, 60 mM KCl, 0.25 M sucrose, 15 mM NaCl, 1 mM CaCl2, 0.8% Triton X100, and as inhibitors of proteases 1 mM phenylmethylsulfonyl fluoride (PMSF), 1 μg/mL aprotinin (see Note 1). 2. 0.4 M H2SO4. 3. Cold acetone (maintained at −20°C). 4. 4 M urea. 5. Liquid nitrogen. 6. Mortars and pestle. 7. Falcon tubes (50 mL). 8. Microcentrifuge tubes. 9. Sterile cheesecloths.

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Table 1 Solutions for SDS PAGE 15% 4× separating buffer

2.3. SDS PAGE

2.5 mL

4× stacking buffer

2.3 mL

Acrylamide (30%)

5 mL

Acrylamide (30%)

0.670 mL

Water

2.5 mL

Water

2.5 mL

APS (10%)

50 μL

APS (10%)

30 μL

TEMED

25 μL

TEMED

15 μL

1. 4× separating buffer: 1.5 M TRIS–HCl, 0.4% (w/v) SDS, pH 8.8. Store at 4°C (see Table 1). 2. 4× stacking buffer: 0.5 M TRIS–HCl, 0.4% (w/v) SDS, pH 6.8. Store at 4°C (see Table 1). 3. 30% (w/v) Acrylamide-bisacrylamide (29.2% (w/v) Acrylamide, 0.8% (w/v) N¢N¢-bis-methylene-acrylamide). 4. 10% ammonium persulfate (APS). Prepare a fresh solution every time. 5. N,N,N ¢,N ¢-Tetramethylethylenediamine (TEMED). 6. 2× SDS sample buffer: 25% of 4× stacking buffer, 20% of glycerol, 10% (w/v) SDS, 5% β-mercaptoethanol, 0.1% (w/v) bromophenol blue. 7. 10× running buffer: 250 mM TRIS base (adjusted pH at 8.5 with HCl), 2 M glycine, 1% (w/v) SDS. 8. Protein molecular weight standard prestained (Bio-Rad) or compatible with other colorimetric and fluorescent detection method. 9. Vertical polyacrylamide gel apparatus Mini Protean System (Bio-Rad) or equipment equivalent and power supply Power Pac HV (Bio-Rad) or equivalent.

2.4. Western Blot

1. Transfer membranes: PVDF (Millipore Immobilon-P). 2. 15% SDS-PAGE gel containing the resolved proteins. 3. Methanol 100%. 4. Pads or equivalent sponge. 5. Filter paper. 6. Transfer buffer: 25 mM TRIS base, 192 mM Glycine, 10% methanol, pH 8.3 (see Note 2). 7. Electroblotting apparatus (Bio-Rad). 8. Power supply Pac HV (Bio-Rad) or equivalent.

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9. 10× PBS buffer (see Table 2). 10. Ponceau-S red 0.005% (Sigma) or any reversible stain. 11. Blocking reagents: non fat dry milk or bovine serum albumin (BSA) or Casein. 12. Antibodies (see Table 3). 13. Chemiluminescent HRP substrate (Millipore). 14. Plastic wrap or plastic bag. 15. Developing cassette.

Table 2 Preparation of Phosphate Buffered Saline (PBS) and Phosphate Buffered Saline Tween-20 (PBST) Reagent

1× PBS

TPBS

Sodium chloride (1.4 M)

8g

8g

Potassium chloride (26.8 mM)

0.2 g

0.2 g

Sodium phosphate dibasic (77.5 mM)

1.1 g

1.1 g

Potassium phosphate (17.6 mM)

0.24 g

0.24 g

Tween-20 (0.5%)

5 mL

pH 7.4 The pH of PBS and TPBS solutions is adjusted with 1 N NaOH. TPBS buffer is used to prepare the blocking solution by adding 3–5% of nonfat dry milk and to prepare antibodies dilution. For washing the membranes, use only TPBS and PBS buffer

Table 3 Dilution of antibodies specific directed against histone H3 methylation at four residues of lysine and respective detection times

Primary antibody Anti-Histone H3 Anti-dimethyl-Histone H3 (Lys4) Anti-trimethyl-Histone H3 (Lys4) Anti-dimethyl-Histone H3 (lys9) Anti-trimethyl-Histone H3 (Lys27) Anti-dimethyl-Histone H3 (Lys 36) Secondary antibody Goat Anti-Rabbit IgG, HRPconjugate

Catalogue number

Dilution in PBST

Detection time

07-690 07-030 05-745R 07-441 07-449 07-274

1:10,000 1:10,000 1:1,500 1:1,000 1:1,000 1:1,000

5–15 s 20–60 s 3–5 min 3–5 min 5 min 3–5 min

12-348

1:20,000

All these antibodies are available from Millipore

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16. X-ray film (Thermo Scientific). 17. Developing Reagents. Solution A: GBX developer, Solution B: GBX fixer (Sigma). 18. Dark room. 19. Gel documentation system (BioRad).

3. Methods 3.1. Histone Isolation

1. Grind 300–500 mg of tissue in N2 liquid into a fine powder using a mortar and pestle and transfer to a Falcon tube and add 10 mL of NIB and maintain for 5 min on ice. 2. Filter the slurry through three layers of sterile cheesecloth and centrifuge the filtrate at 10,000 × g for 20 min at 4°C. 3. Resuspend the pellet with 2 mL of 0.4 M H2SO4 and vortex for 20 s; centrifuge the homogenate at 10,000 × g for 10 min at 4°C. 4. Transfer the supernatant to a new tube (the pellet is extracted twice; repeat step 3). 5. Precipitate proteins with 10–12 volumes of cold acetone and keep at −20°C for 12 h (see Note 3). 6. Centrifuge the precipitate at 13,000 × g for 30 min at 4°C and carefully discard the supernatant and air-dry the pellet to remove the residual acetone. 7. Resuspend the pellet with 200 μL of 4 M Urea by vortexing until the pellet is dissolved. 8. Take 5 μL of sample to quantify total protein and store the samples at −20°C until used.

3.2. Protein Separation and Transfer

1. Five microgram of protein with 10 μL of 2× SDS buffer must be heated at 100°C for 5 min. The proteins are resolved by electrophoresis in a 15% SDS-PAGE gel. One of the gel wells should include a protein molecular mass marker and a positive control for histones such as calf thymus histone. The electrophoresis is carried out at 100 V for 90 min (see Table 1 for details SDS-PAGE and see Note 4). 2. After the electrophoresis has been completed, remove the gel from the cassette and remove the stacking gel. 3. Take the gel and immerse it in the transfer buffer to equilibrate the gel for 10 min (see Note 5). 4. For each gel, cut the blotter paper to fit the transfer cassette.

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5. Prepare the membrane for transfer: (a) PVDF membrane: cut the membrane to fit in the transfer cassette and soak it in 100% methanol for 15–20 s. (b) To remove the excess of methanol, place the membrane for 2 min in distilled water. (c) Nitrocellulose membrane: do not soak in methanol. (d) Place both types of membranes in the transfer buffer for 5–10 min. 6. Transfer cassette assembly (see Fig. 2a and Note 6): (e) Open the cassette holder. (f ) Place a pad on one side of the cassette. (g) Place two layers of blotter paper previously wet in transfer buffer. (h) Carefully place the gel with the proteins resolved and the molecular marker standards at the right side. (i) Carefully place the membrane on top of the gel. (j) Place two layers of blotter paper on top of the stack. (k) Place a second pad on top of the blotter paper and close the cassette holder. 7. Place the cassette holder containing the gel and membrane into electroblotting apparatus with the membrane side to the anode (+) and fill the tank with the transfer buffer. 8. The transference of the proteins was done in 3.5 h at 265 mA at 4°C.

Fig. 2. Transfer protein and chemiluminescence principle. (a) The acrylamide gel where the proteins are resolved and the membrane are placed in the middle of two layers of blotter papers and two pads. The gel is kept faced to the anode side and then the whole assembly is placed in the electroblotting apparatus and the transfer carried out at 265 mA for 3.5 h at 4°C. (b) After protein (P) has been transferred to the membrane, all the unoccupied spaces in the membrane need to be blocked by a blocking agent (nonfat milk). The membrane is then exposed to an antibody which recognizes a specific protein in the membrane, and then the blot is probed with a second antibody that recognizes the first antibody. This second antibody is coupled to an enzyme (E) which converts the substrate (S) into a luminescence signal that produces a mark in the film that indicates the presence, abundance, and position of the protein of interest.

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9. After the transference has been completed, remove the cassette holder from the tank and disassemble. 10. Carefully rinse the membrane with distilled water to remove gel remains. 11. Stain the membrane to verify the transfer efficiency: (l) Ponceau-S red: dissolve 0.5 g in 1 mL glacial acetic acid and bring to 100 mL with distilled water. (m) Soak the membrane with the Ponceau-S red solution for 1 min or until the proteins are visible. (n) Remove the membrane and rinse thoroughly with water until the desired contrast and document. (o) Remove the stain with 0.1 N NaOH and wash the membrane two times with PBS buffer and continue with the immunodetection. 3.3. Immunodetection (Antibody Incubations)

1. The dilution of antibodies is detailed in the Table 3. 2. Place the membrane blocking buffer (1× PBS, 0.5% Tween-20, 3–5% non fat dry milk) and incubate it for 1 h with slow agitation at room temperature. 3. Wash the membrane three times with TPBS for 5 min each (see Table 2). 4. Incubate the membrane in the primary antibody solution for 1 h at room temperature or overnight at 4°C with constant agitation. 5. Wash the membrane at least two times for 5 min with PBST and one time with PBS. 6. Incubate the membrane in the secondary antibody solution for 30 min at room temperature with constant agitation. 7. Wash the membrane three times with PBST for 5 min each and one time with PBS. Additional washes may further background. 8. Proceed with the chemiluminescent detection (see Fig. 2b).

3.4. Chemiluminescent Detection

1. Prepare the agent chemiluminescent substrate following the manufacturer’s instructions (Chemiluminescent HRP substrate of Millipore). 2. Remove the PBS and add the substrate to completely cover the membrane. 3. Drain the excess substrate and cover the membrane with plastic wrap, avoiding bubble formation. 4. Expose the membrane to X-ray film and place it into the film cassette in the dark room. A red light could help inside the dark room. The times of exposure is detailed in Table 3. 5. Remove the film cassette and take out the film.

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Fig. 3. Analysis of histone H3 methylation. (a) Separation of total nuclear proteins on a 15% SDS-PAGE gel stained with Coomassie R-250. Line 1: leaf of in vitro Agave fourcroydes, Line 2: leaf of in vitro Coffea canephora, Line 3: Positive control of histone H3 from calf thymus. The head rows indicate the histone H3 in the samples. (b) Immunodetection of histones H3 (top) and H3K4m2 (bottom) isolated from leaf and embryo of C. canephora. (c) Immunodetection of histones H3 (top) and H3K4m2 (bottom) isolated from leaves of two different plants of A. fourcroydes.

6. Place the film in a developer solution to obtain the desire contrast, then wash quickly in water and soak the film in the fixative solution, and then wash the film again in water (see Note 7). 7. Photodocument the film (see Fig. 3). 3.5. Membrane Stripping and Retesting

1. After exposing the membrane to the film, wash the membrane twice with TPBS for 5 min each. 2. Place the membrane in stripping solution (25 mM glycine, 1% SDS, adjust pH to 2 with HCl), gently shaking for 15 min at room temperature (two times). 3. Wash the membrane two times with TPBS for 5 min each. 4. Repeat the steps 3–9 of Subheading 3.3 and all Subheading 3.4. 5. The membrane retesting can be done up to five times.

4. Notes 1. All stocks solutions of NIB should be kept at 4°C. All the extraction steps should be carried on ice. PMSF stock: prepare a 200 mM solution in ethyl alcohol absolute and store it at 4°C. Aprotinin stock: prepare 1 μg/mL solution in water and store it at −20°C.

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2. This solution can be prepared as 10× stock and adjust the pH to 8.3. Add the methanol prior to use. 3. This step guarantees the best histone precipitation, particularly when the sample is small. 4. The proteins markers prestained can help to visualize the transference into the membrane and the molecular mass of the histones after the film has been exposed. 5. Gel equilibration prevents a change in the gel size during the transference time and avoids formation of bubbles during the transference. 6. Always use gloves when manipulating gels and use sterile forceps for the membrane or blotter paper to avoid false positives. To ensure an even transference to the membrane, remove any air bubbles between layers. 7. If a high background exists in the film, it is needed to increase the concentration of the blocking reagent, extend the washings time, or decrease the concentration of the secondary antibody.

Acknowledgments We gratefully acknowledge the funding from L’Oréal-UNESCOAMC. References 1. Vaquero A, Loyola A, Reinberg D (2003) The constantly changing face of chromatin. Sci Agni Know Env 4:1–16 2. Bowler C, Benvenuto G, Laflamme P et al (2004) Chromatin techniques for plant cells. Plant J 39:776–789 3. Cheung P, Lau P (2005) Epigenetic regulation by histone methylation and histone variants. Mol Endocrinol 19:563–573 4. Kouzarides T, Berger LS (2007) Chromatin modifications and their mechanism of action. In: Allis CD, Jenuwien T, Reinberg D et al (eds) Epigenetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp 191–209 5. Zhang K, Sridhar V, Zhu J, Kapoor A, Zhu JK (2007) Distintive core of histone post-translational modification patterns in Arabidopsis thaliana. PLoS One 11:1–11 6. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705

7. Yang W, Jiang D, Jiang J et al (2010) A plantspecific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis. Plant J 62:663–673 8. Liu C, Lu F, Cui X et al (2010) Histone methylation in higher plants. Annu Rev Plant Biol 61:395–420 9. Xu L, Zhao Z, Dong A et al (2008) Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana. Mol Cell Biol 28:1348–1360 10. Jackson J, Johnson L, Jasencakova Z et al (2004) Dimethylation of histone H3 lysine 9 is critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112:308–315 11. Jacob Y, Feng M, LeBlanc C et al (2009) ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure

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a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112:308–315 Amasino R (2010) Seasonal and developmental timing of flowering. Plant J 61:1001–1013 Bruce T, Mazur E, Napier J et al (2007) Stressful “memories” of plants: evidence and possible mechanisms. Plant Sci 173:603–608 Martienssen RA, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293:1070–1074 Verdeil JL, Alemanno L, Niememack N et al (2007) Pluripotent versus totipotent plant stem cells: dependence versus autonomy? Trends Plant Sci 12:245–252 Shen WH, Meyer D (2004) Ectopic expression of the NtSET1 histone methyltransferase inhibits cell expansion, and affects cell division and differentiation in tobacco plants. Plant Cell Physiol 45:1715–1719 Liang YK, Wang Y, Zang Y et al (2003) OsSET1, a novel SET-domain-containing gene from rice. J Exp Bot 54:1995–1996 Ding Y, Wang X, Su L et al (2007) SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. Plant Cell 19:9–22 Quiroz-Figueroa FR, Monforte-González M, Galaz-Avalos RM et al (2006) Direct somatic embryogenesis in Coffea canephora. In: LoyolaVargas VM, Vázquez-Flota FA (eds) Plant cell culture protocols. Humana, Totowa, NJ, pp 111–117

Chapter 25 Basic Procedures for Epigenetic Analysis in Plant Cell and Tissue Culture José L. Rodríguez, Jesús Pascual, Marcos Viejo, Luis Valledor, Mónica Meijón, Rodrigo Hasbún, Norma Yague Yrei, María E. Santamaría, Marta Pérez, Mario Fernández Fraga, María Berdasco, Roberto Rodríguez Fernández, and María J. Cañal Abstract In vitro culture is one of the most studied techniques, and it is used to study many developmental processes, especially in forestry species, because of growth timing and easy manipulation. Epigenetics has been shown as an important influence on many research analyses such as cancer in mammals and developmental processes in plants such as flowering, but regarding in vitro culture, techniques to study DNA methylation or chromatin modifications were mainly limited to identify somaclonal variation of the micropropagated material. Because in vitro culture is not only a way to generate plant material but also a bunch of differentially induced developmental processes, an approach of techniques and some research carried out to study the different changes regarding DNA methylation and chromatin and translational modifications that take place during these processes is reviewed. Key words: Bisulfite sequencing, ChIP, Chromatin, DNA methylation, Histone PTMs, In vitro tissue culture

1. Introduction In plants, cell plasticity enables somatic cells to begin new developmental programs generating adventitious organ formation in presence of the appropriate plant growth regulators. Somatic embryogenesis and adventitious shoot formation are practical examples of cell reprogramming (1, 2), which are negatively affected by ontogenic and physiological age, both constitute important tools to propagate selected genotypes in breeding programs. Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_25, © Springer Science+Business Media, LLC 2012

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Plant cell culture techniques are a source of epigenetic variation, especially those which involve and indirect organogenesis through a callus stage (3, 4), causing transposon reactivation and epigenetic changes focused on genes, such as epiallele formation (5, 6), leading to heritable changes in gene expression (7). Understanding of mechanisms that regulate cell plasticity is essential from a basic point of view of developmental processes and from an applied point of view regarding the biotechnological importance of morphogenesis manipulation. These processes involve the establishment of new gene expression patterns and changes in epigenetic plasticity, making this process a suitable experimental system to study loss of competence regarding development as well as to analyze epigenetic changes regarding ontogenic state (8). Epigenetics is defined as “heritable changes in gene expression that occur without a change in DNA sequence” (9), and can be understood as a system to selectively regulate genome information through activating or inactivating gene expression. At a molecular level, DNA methylation, posttranslational histone modifications, chromatin remodeling factors, transcriptional factors, and chromosomal proteins cooperate together. Although the mechanisms of chromatin regulation are less studied in plants, advances in their research have shown that they share similarities with other eukaryotes in chromatin remodeling factors, histone acetylation/deacetylation and methylation/demethylation, and DNA methylation/demethylation and at a gene level as well (10). Chromatin is not just a static method for packing DNA but also a dynamic strategy that cells use to respond to environmental stimuli. The precise control of chromatin modification in response to developmental and environmental cues determines the correct spatial and temporal expression of genes. The differences among epigenetic modifications are a precise cross talk; variations in DNA methylation have an effect in histone deacetylation and methylation affecting chromatin structure in animals (11, 12) and in plants (13). To understand their influence on a specific physiological situation, an overview of the different modifications with a correct interpretation of the individual data must be done. In this chapter, we show the main techniques used for the analysis of DNA methylation (global and site-specific) and chromatin modifications from histones and transcription factors focusing more on the results than on the techniques achieved in plant cell and tissue culture as well as on several developmental processes by Epiphysage Research Group.

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2. DNA Methylation Methylation at position 5 of cytosines is the main epigenetic modification in eukaryotes, and alterations in DNA methylation are frequently involved in transcriptional gene regulation. Its presence and quantification was first time described in mammals and plants in the 1950s (14, 15). Methylation generally represses transcription in two ways: blocking transcription factors binding and modifying nearby histones and therefore chromatin structure (16). Cytosine is primarily methylated in the CG dinucleotide called CG islands, but plants unlike animals have a high amount of 5-methylcytosine, suggesting that methylation is not restricted to the CG sequence, and it was also found that CNG and, less abundantly, CNN sequences were susceptible of cytosine methylation (17). Recent advances in whole genome methylation profiling technologies have caused a great interest in analyzing cytosine methylation levels and distribution within the genome, allowing us to better understand various developmental processes, like in vitro plant culture. Some reviews about DNA methylation analysis techniques have been done (18, 19), but the increasing number of scientific research about DNA methylation in plant development, and to a lesser extent in plant in vitro culture, encouraged us to see the influence of DNA methylation on this process. 2.1. Global DNA Methylation

It is widely accepted that DNA methylation controls differentiation maintaining cell status stability (20), and global methylcytosine content in genomic DNA varies widely across species, organs, and developmental states. Epigenetic modifications, and in particular DNA hypomethylation, are suspected of being responsible for somaclonal variation (6), being growth treatments and environmental stress proposed as main factors in this variation (21). Although genetic stability is certified by conventional DNA markers, no uniform clone regenerants are often obtained, being this variation caused by different DNA methylation levels. The analysis of global methylated DNA can be measured by the content of 5-mdC or by its distribution along the tissue.

2.1.1. HPLC-MS and HPCE-MS (High-Performance Liquid Chromatography-Mass Spectrometry, HighPerformance Capillary Electrophoresis-Mass Spectrometry)

Quantification of 5-methyldeoxycytosine genomic DNA methylation establishes certain degrees of global DNA methylation which can be used as markers for developmental or physiological processes (22). The analysis of global DNA methylation can be performed by HPCE (23, 24) or by HPLC (25, 26); both methods share the enzymatic hydrolysis of the DNA strands and a phosphatase alkaline treatment, to obtain deoxynucleosides; these deoxynucleosides are run in a HPCE or HPLC system, and the peaks obtained are measured by the following formula % 5-mdC = 5-mdC peak area/(5-mdC + 5-dC peak areas; Fig. 1).

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Fig. 1. High-performance capillary electrophoresis electropherogram of Pinus radiata genomic DNA. Each peak belongs to a different nucleoside. C corresponds to 5-dC and mC corresponds to 5-mdC.

It has been shown that different levels in global DNA methylation are essential for a correct response of plant material to in vitro culture (27), and it seems that both 5-mdC amount and physiological state of the plant have a key influence on the success of the culture, even different tissues in the same organ (28–30). Global DNA methylation has been proposed as an epigenetic marker in different developmental situations (31, 32), although there is some disagreement about the levels of DNA methylation and the age of the explants depending on the species (33–35). 2.1.2. Antibody-Based Detection

Global DNA methylation can be also quantified by ELISA, and many commercial kits are available. In our experience, these kits are quite inaccurate because the standards technical design is based on mammal DNA, so we focus on spatial distribution of DNA methylcytosine along the tissue. It is also necessary to know which cells contain methylated DNA, the number of cells, their location, and the evolution of the DNA methylation pattern of the tissue during ontogenic development. Histological analyses based on DAPI staining of cell nucleus and fluorescent immunolocation of 5-mdC is used (36).

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There is no bibliography related to in vitro culture, but several studies related to which organ response to organogenesis and the epigenetic status of the tissues is available. In P. radiata needle development, responsive immature needles showed less labeling in palisade layers, while mature needles are strongly labeled. Similar responses are also observed in other organ maturation processes, such as flower development, in which 5mdC layout increases with the differentiation of their productive organs (36–39) or during bud dormancy in C. sativa, in which 5mdC layout increases with the bud dormancy and decreases during bud burst (40). Some research in adventitious caulogenesis in P. radiata zygotic embryos done in our research group, shows that main changes in DNA methylation labeling are focused in meristematic tissues in the early steps of the process but the tissues responding to the treatment are affected in the later steps (Fig. 2a). 2.2. Restriction Enzyme DNA Methylation Patterns

Analysis of DNA by restriction enzyme has been widely used to identify somaclonal variation in micropropagated species and many molecular markers has been used (41, 42). These variations have been also studied using methylation-sensitive restriction enzymes, Hpa II and Msp I; isoschizomers are usually the most used enzymes to make these analysis, having one common procedure by an adaptor ligation and a later PCR amplification (6).

2.2.1. Microarray-Based DNA Methylation Profiling

These methods are high-throughput DNA methylation screening tools, which performs a methylation-sensitive restriction enzyme treatment and a hybridization of a CpG island microarray to make a profile of methylated fragments (43). This technique is widely used in human cancer research because of the availability of CpG island databases that allow you to design a custom microarray or use a commercial one (44, 45).

Fig. 2. Merged image of indirect immunolocalization in nuclei of Pinus radiata embryos of 5-methyl cytosine (a) and acetylated histone H4 (b) (green color) and nuclei stained with DAPI as a positive control (blue color). Light blue corresponds to overlaid secondary antibody and DAPI signals. Scale bar 300 μm.

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2.2.2. MS-AFLP, HELP, MS AP PCR/MSRF, MS-RDA, MCA-RDA, AIMS, and RLGS (Methylation Sensitive Amplified Fragment Length Polymorphism/HpaII Tiny Fragment Enrichment by Ligation-Mediated PCR, Methylation-Sensitive Arbitrarily Primed PCR/ Methylation-Sensitive Restriction Fingerprinting, Methylation-Sensitive Representational Difference Analysis/ Methylated CpG Island AmplificationRepresentational Difference Analysis/ Amplification of Intermethylated Sites, Restriction Landmark Genomic Scanning)

These techniques and many others such as MS-RFLP (46) are based on the band amplification profile after PCR. Depending on the technique and the primers used, the profile of bands can vary from a few bands to many of them (47, 48). A later on analysis of the data reveals methylation and demethylation events because of the difference in the experimental situation. They have been used mainly in plant in vitro culture to make an epigenetic certification of micropropagated plant (29) and to identify DNA sequences that suffer changes in its promoter region, related probably to the in vitro culture process (49, 50).

2.3. Genome-Wide DNA Methylation

5mC marks can selectively be detected through the genome using specific antibodies and proteins that selectively bind 5mC (51, 52). These methods are relatively straightforward and do not require either digestion of genomic DNA or bisulfite treatment. The basis of these methods is the enrichment of a fraction of DNA in methylated DNA; this population of DNA fragments can follow two main analysis strategies identifying the sequences of the enriched fraction by mass sequencing and hybridizing a microarray seeing the differential amount of each sequence.

2.3.1. MeDIP, MIRA, MBD Columns (Methylated DNA Immunoprecipitation/ Methylated CpG Island Recovery Assay)

For this kind of analyses, DNA is fragmented in a size range about 200–1,000 bp by enzyme restriction or by mechanical methods, and a later precipitation is done using a 5-methyl cytosine antibody or a methylated-CpG binding domain (MBD) protein, being MBD2B, the shorter protein isoform of MBD2 family which possesses the highest affinity to methylated DNA among the MBD proteins the most used (53, 54).

2.4. Individual CpG Analysis

The study of known promoters of sequences of interest can be tackled by quantitation of methylation at individual CpG sites (47, 55). These techniques rely on the fact that restriction digestion can be used to reveal DNA methylation-dependent sequence differences in PCR-amplified bisulfite-treated genomic DNA and that these differences can be applied to specific loci. Methylation levels

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in the original DNA sample are represented by the relative amounts of digested and undigested PCR product in a linearly quantitative fashion across a wide spectrum of DNA methylation levels. 2.4.1. COBRA, MS-SNuPE, MSO, and Real-Time MSP (Combined Bisulfite Restriction Analysis, Methylation-Sensitive Single Nucleotide Primer Extension, MethylationSpecific Oligonucleotide Array, Methylation-Specific PCR)

These techniques are the first ones which involve a DNA modification in the sequence, by a modification of unmethylated cytosine into uracil, while methylated cytosine (both 5mC or 5hmC) remains unchanged (56). This change in the DNA sequence following bisulfite conversion can be detected by two different approaches, a combination with methylation sensitive enzymes or by direct sequencing. The use of bisulfite-converted DNA for DNA methylation analysis has surpassed almost every other methodology for DNA methylation analysis of site-specific CpG islands. This sequence conversion can lead to the methylation dependent creation of new restriction enzyme sites or old sites can still remain in case of cytosine is methylated. Specific primer design can show us an amplification of a mixture of methylated and unmethylated CpGs that will be resolved in a polyacrylamide gel (55, 57) or hybridizing an oligonucleotide microarray with specific sequences that match for unmodified cytosines and for the modified ones, calculating the relative amount of each (58). Methylation Specific PCR differs from the other techniques in the absence of restriction enzymes and in the design of the primers, in this case the primer is located in the region where CpG are present and next to the 3 end to provide a higher degree of mispairing in the PCR (59).

2.4.2. MethyLight, QAMA (Quantitative Analysis of Methylated Alleles)

These techniques are claimed to be high-throughput methylation analysis and are based on the same principles as previous ones, that is to say, sodium bisulfite treatment and a PCR reaction. The difference relies in that this method is a sensitive, fluorescence-based real-time PCR technique that is capable of quantitating DNA methylation at a particular locus. The use of a fluorescent probe inside the PCR product sequence and the 5 to 3 exonuclease activity of the polymerase, release the fluorophore that is next to a quencher already present in the probe. Both the primers and the probe have CpG dinucleotides in their sequence (60). However, the availability of a new kind of probes, which differentiate a single base pair change, based on the minor groove binder technology (61) allows the quantification of methylated alleles more accurately. The use of two probes, one of them designed for unmethylated DNA and the other designed for methylated DNA, is the difference with MethyLight (62).

2.5. Sequencing DNA Methylation

Direct bisulfite sequencing was first time used by Frommer in 1992 (63) to identify the nucleotides resistant to bisulfite conversion. After DNA conversion, a suitable couple of primers must be designed free of CpG dinucleotides (64); however, all programs for bisulfite primer design are reduced exclusively to mammal DNA and therefore to CpG dinucleotide, so primer design for plant DNA could be a cumbersome job sometimes. This technique requires cloning of the

2.5.1. Sanger Sequencing, Pyrosequencing

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PCR product prior to sequencing for adequate sensitivity because a mixture of different populations of differential methylated cytosines along the sequence is present. In the chromatogram results all sites of unmethylated cytosines are displayed as thymines in the resulting amplified sequence and methylated ones remain being cytosines. This technique has been widely used in plant tissue culture to control transposon activation and monitor specific promoter methylation status of interest genes (65, 66). After DNA bisulfite modification and PCR amplification of the region of interest, pyrosequencing is used to determine the bisulfite-converted sequence of specific CpG sites in the region. The technique detects the amount of C and T incorporated during the sequence extension being very precise with the relative amount of each one (67). The main limitation of this method is that only around 50 nucleotides are sequenced accurately, so a low number of CpGs are analyzed. 2.6. Regional DNA Methylation Levels 2.6.1. Denaturing HPLC

Denaturing high-performance liquid chromatography (DHPLC) (68) analyzes the overall degree of methylation of a region through differential elution profiles based on temperature-dependent resolution of heteroduplexes from homoduplexes; for DNA methylation analyses, the modification with sodium bisulfite provides the heteroduplexes to analyze. This method does not give any information about the methylation status of individual CpGs, but several improvements have been done to detect other molecular markers at the same time (69). DNA methylation plasticity is a major factor involved in plant development and in vitro culture response. Methylation increases with age, phase change, or culture period and is normally associated with a lack of organogenesis potential. Its analysis has undergone a revolution, and enzyme-based and affinity enrichment-based DNA methylation analysis techniques have provided a lot information in genome-wide analysis. High throughput sequencing has become a revolutionary tool for the analysis of methylated DNA. In nonrepeat regions, 5mC can now be mapped with precision by genome-wide bisulfite sequencing revealing the role of DNA methylation along gene promoter or coding sequence. The next step in methylation analysis is to identify the methylome in specific physiological situations and compare the data to that obtained by transcriptomic or proteomic techniques.

3. Chromatin Modifications Chromatin is the state in which DNA is packaged within the cell. The core histones present in the nucleosome, are predominantly globular except for their N-terminal tails, chromatin remodeling factors in histone modifications act by covalently altering the charge

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of hydrophobicity of specific amino acids on histone tails. These modifications alter cis-regulatory elements binding to DNA and act by modifying other chromatin regulators (70). There is a myriad of possible modifications carried out by a gene complex network (71), but all of them, because of the different responses they cause, cannot be present at the same time, so its variations along a process determine a specific chromatin state (72). To study chromatin, there are several protocols depending on the nucleosome distribution, proteins involved, or their modifications (18). 3.1. Genomic Profile of Histone PTMs 3.1.1. Global Quantification

A general overview of a determined histone modification is essential to know its possible role along a process and along the tissue. Up to date, these techniques allow us to identify from a single histone modification to a group of modifications in different histones (73, 74).

3.1.2. HPLC-MS, Antibody-Based Detection

Genome-wide histone analysis, as well as global DNA methylation levels, reveals a general behavior of the studied characteristic and uses it as a marker in the physiological process. Mass spectrometry is a chemical analysis technique that exploits the physical properties of ions to determine their mass to charge ratio (m/z) and a variety of methods can be used to make the analysis after HPLC procedure (75). Histones can be easily extracted from cells, and reproducible separation of histone family members can be achieved on C8- or C18-based columns using reverse-phase high-performance liquid chromatography (RP-HPLC) (76). Individual fractions of the histones are enzymatically digested and analyzed by PMF (Peptide Mass Fingerprint), MS/MS (tandem MS), CAD (Collisionally Activated Dissociation), and ETD (Electron Transfer Dissociation) (77–79). Western blot histone PTMs have been widely analyzed, and in the field of plant in vitro culture we have many references mainly devoted to monitor chromatin remodeling (3, 49). On the other hand, to study the distribution in the different tissues of an organ, immunolocalization is an easy and an informative technique (Fig. 2b) (27, 37).

3.1.3. Genome-Wide Analysis

Cells of multicellular organisms are genetically identical but structurally and functionally different because of the differential expression of their genes. These differences are, in part, consequence of an epigenetic control. DNA methylation and histone PTMs are among the best studied epigenetic regulators. Gene expression depends on DNA–protein interactions, by itself and by the potential possibility that it happens related to DNA accessibility. For this reason, developing methods and techniques to study protein–DNA interactions have been, are and will be focused to the study different genomic processes, such as DNA replication, recombination, repair, and transcription. In this way, chromatin immunoprecipitation is one of the most powerful tools in the characterization of protein modifications and in vivo DNA–protein interactions (80).

Chromatin Immunoprecipitation ChIP

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ChIP procedure consists of discrete steps including in vivo cross-linking of proteins to DNA with formaldehyde, isolation of chromatin from isolated nuclei, shearing of chromatin into small fragments from 200 pb to 800 pb by ultrasound or micrococcal nuclease (MNase) digestion, immunoprecipitation with specific antibodies to DNA-bound proteins, release of the coprecipitated DNA, and finally, PCR amplification with specific primers to determine whether DNA sequences of interest have been precipitated. The latter steps involve comparison of the signal obtained from RT-qPCR signals from the precipitated template with positive and negative controls (80–83). Nonetheless, ChIP has inherent limitations that must be known. Thus, utilization of highly specific antibodies is critical, as it can give false-negative signals. Another source of false-negative signals can be epitope disruption during chromatin cross-linking and shearing. On the other hand, false-positive signals may arise because of formaldehyde may fix transiently, or even nonspecifically, adjacent proteins. As a result, cross-linking fit and calibration curves build to determine the optimal amounts of antibody and chromatin to be used are recommended. Previous recommendations show that ChIP procedures are very sensitive (80). First protocols for ChIP assays were developed and described for mammals, yeast, and Drosophila, but structural anatomical differences between plant and animal cells make impossible the direct application of animal ChIP protocols to plants. Some modifications and additional procedures, such as vacuum fixation, that has been introduced to ensure penetration of the DNA–protein cross-linking solution into plant cells, are need. The presence of large vacuoles in mature plant cells is another capital item, giving as result a relatively low yield of isolated nuclei per gram of starting tissue. They are also a source of proteolytic enzymes, so special attention during isolation procedures and use of healthy fresh plant tissues are required. As a result, plant-specific ChIP protocols have been developed and used for analyzing a large number of epigenetically controlled genes in plants, as it is the case of our research group, EPIPHYSAGE (http://www.uniovi.es/epiphysage/), in which we use ChIP approach in gene-specific epigenetic regulation studies related to P. radiata cell suspension cultures and abiotic stress. SAGE, SACO, GMAT, PET, Seq (Serial Analysis of Gene Expression, Serial Analysis of Chromatin Occupancy, Genome-Wide Mapping Technique, Paired-End Ditag Sequencing, Massive Sequencing)

In the past few years, various sequencing-based protocols have been developed to analyze ChIP samples (84). They are known as ChIP downstream protocols, combining ChIP with gene expression and sequencing analysis. The most commonly used techniques are ChIP + serial analysis of gene expression (ChIP-SAGE, GMAT) (85, 86), ChIP + serial analysis of chromatin occupancy (ChIPSACO) (87, 88), ChIP + genome-wide mapping technique (ChIPGMAT), and ChIP combined with paired-end ditag sequencing (ChIP–PET) (89). The most recent technique combines ChIP

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with massively parallel sequencing (ChIP–Seq). It allows for genome-wide analysis in less time and high-throughput studies, which is going to unveil new aspects of plant development biology in the next years (90). Application of these techniques has led to great advances in our understanding of how epigenetic phenomena are regulated and how they affect gene expression. Nowadays, the most useful technique used to map histone modifications at a genomic scale has been ChIP combined with DNA microarrays (ChIP–chip) (91), in which chromatin fragments are differentially immunoprecipitated with a specific antibody and then are amplified and fluorescently labeled to be hybridized in a DNA microarray. The first ChIP-chip studies of histone modifications in Saccharomyces cerevisiae and Drosophila melanogaster suggested that histone modifications are associated with distinct genomic regions and with distinct transcription states. In plants, ChIP-chip approach has been used with similar purposes (92), but in many species the inexistence of complete sequenced genome is a limitation. Another downstream ChIP technique that combines this with SAGE is GMAT, which is also known as ChIP–SAGE (http://www.sagenet.org). Briefly, first the procedure begins with already mentioned ChIP procedure, second a biotinylated universal linker is ligated to DNA ends, which are bound to streptavidin beads, third DNA is digested with NlaIII and ligated to linkers containing recognition sequence of MmeI, and fourth MmeI digestion produces 21–22 pb sequence tags of the immunoprecipitated DNA, which are concatenated, cloned in a vector, sequenced, and mapped by hybridization with a reference genome, correlating directly the number of tags detected at a genomic region with the modification level of this. Thus, the results obtained from GMAT might be more quantitative than ChIP–chip, though these two techniques have not yet been directly compared (84). ChIP–Seq is a recently developed technique for analyzing ChIP DNA using a high-throughput massively sequencing technique and was one of the early applications of the technology called “next-generation sequencing” (93). The immunoprecipitated DNA is ligated to a pair of adaptors and hybridized on a solid surface with covalently bonded oligos, which are complementary to the adaptor sequences. A sequence ranging 35 bp is generated by a “sequencing-by-synthesis” technique, a modified Sanger sequencing procedure. In this technique, the number of sequenced reads that are mapped to a genomic locus is directly proportional to its modification level. Obtained ChIP-Seq results are more quantitative than those from ChIP-chip. Each of the methods discussed above relies on ChIP experiments to examine specific modifications, but several points need to be kept in mind when interpreting ChIP results. Antibody specificity

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depends on immunoprecipitation results, the different methods used for chromatin preparation such as sonication or microccocal nuclease digestion must be considered, and finally, ChIP requires high amounts of DNA, using hundreds of thousands or even millions of cultured cells. As well as a transcriptome, results obtained are a snapshot of the histone modification status, which varies along time and experimental situation, making difficult to work with heterogeneous tissues. 3.2. Genomic Profile of Nucleosome Distribution

Nucleosomes are essential in eukaryotes for DNA packaging and telomere function (94, 95). The DNA strand is wrapped around this protein complex, form by two copies of histones H2A, H2B, H3, and H4. Their distribution in the chromatin, the histone Posttranslational modifications, and DNA methylation determine the accessibility for the expression of the regions of the genome under its control (96). Thus, chromatin status (euchromatin or heterochromatin) and epigenetic modification will lead to gene expression or repression, respectively. Regarding the position of the nucleosomes along the genome, it is believed that less amount of them have a fixed position predicted by DNA sequence, and the rest does not follow this pattern (90); some authors relate these fixed nucleosomes to low plasticity genes and others to high plasticity genes (97). Recently, studies in Arabidopsis related to gene expression show a correlation between nucleosome status and plant heat responses. It seems that modifications of chromatin led by nucleosome density (98) and substitution of histone H2A by Histone H2A.Z (99) play an important role in heat-related gene expression. Nucleosomes are an essential actor by taking part in the epigenetic regulation of genome expression and chromatin packaging during cell division; no studies have been carried out focusing into its relation with the control of gene expression during in vitro culture.

3.2.1. Micrococcal Nuclease Analysis of Chromatin Structure

This technique is used to map nucleosome position and spacing along the genome, this enzyme is known to cut between nucleosomal spaces. There are two ways to isolate nucleosomes after cutting cross-linked DNA: The first of them is an immunoprecipitation with an antibody against a histone, which has been already described in the previous paragraphs, and the second one is based on the isolation of mononucleosomal DNA bands from a low melting point agarose gel (100).

3.3. Transcription Factor PTMs

There are many transcription factors related to in vitro culture process, and the techniques to analyze them are similar to the previously described immunoprecipitation techniques such as ChIP but against a transcription factor; however, no results have been found

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related to plant in vitro culture, although the production of specific antibodies against new transcription factors will allow researchers make these studies soon. Identifying the position where protein complexes join DNA can be detected with this technique (101), and there is a statistical approach based on Kernel Density Estimation approach, which utilizes ChIP-Seq data, named QuEST (102).

4. Small RNAs (miRNA and siRNA)

The Small RNAs (sRNAs) constitute a family of regulatory noncoding RNAs (ncRNAs) of 19–28 nt in length, derived from double-stranded RNAs (dsRNAs) and are highly conserved evolutionarily across species. There are two main classes of small RNAs involved in RNA silencing: microRNAs (miRNAs) and small interfering RNAs (siRNAs); the classification depends on the biogenesis and not on their action (103, 104). These sRNAs come from the long single-stranded RNA (ssRNAs) and are processed by RNAse III proteins. They are involved in several processes including DNA elimination, heterochromatin assembly, mRNA cleavage, and translational repression related to developmental processes and response to stress (105). To study sRNAs, there are many protocols and commercial kits to extract them, and the identification of the different families is in progress (106). Because these sequences have a homology with their targets, there are different procedures to predict them, giving as result conserved targets among species (107). Regarding in vitro culture, there are some research related to transposable elements and the induction of transcription of siRNAs during cell suspension cultures (108), and new research has been done in relation to expression of miRNAs climatic adaptation and epigenomic imprinting even through an in vitro culture step probably related to DNA methylation (109).

5. Conclusions Epigenetics is an important factor with a huge influence on many development processes, and its analysis appears to be essential in their regulation. In vitro culture as a developmental process is also affected by the different epigenetic modifications, and although several techniques have been used to identify somaclonal variation or global methylation content widely, recent techniques open a gate to unravel the function of specific genes or gene families and their regulation during this complex process.

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Chapter 26 Plant Tissue Culture and Molecular Markers María Tamayo-Ordoñez, Javier Huijara-Vasconselos, Adriana Quiroz-Moreno, Matilde Ortíz-García, and Lorenzo Felipe Sánchez-Teyer Abstract Tissue culture can be used to propagate elite material or to generate new variability by employing somaclonal variation. Genetic stability of the process must be evaluated analyzing DNA profiles by the use of molecular markers. Several techniques have been reported for the screening of genetic variation on tissue culture derived material; however, a highly informative and good relation among the time–cost–information is obtained using Amplified Fragment Length Polymorphism (AFLP) in automatic sequencer. This technique involves a double-digestion of DNA with restriction enzymes, ligation of adapters at both extremities of the restriction fragments, and finally, selective polymerase chain reaction (PCR) amplification of the fragments. A semiautomatic process for the analysis could be used, but several considerations must be taken into account before such a use. Key words: AFLP, Fingerprint, Genetic stability, Genetic screening, In vitro variability, Somaclonal variation

1. Introduction Tissue culture can be used to propagate elite material or generate new variability by somaclonal variation (SV), a term used to define the variability induced by tissue culture (1) which is a result of a combination of both genetic and epigenetic variation (2). The level of such variability can be evaluated using molecular markers. Several techniques of molecular markers can be mentioned such as AFLP, RAPD, SSR, SSAP, etc.; all of them evaluate changes at the DNA level based on PCR amplification using specific primers, and in some cases addressed to amplify repetitive elements on the genome. Amplified fragment length polymorphism (AFLP) is a widely used technique to detect variability comparing the regenerated plants with the parental material, involving a process that includes the Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_26, © Springer Science+Business Media, LLC 2012

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double-digestion of DNA with restriction enzymes, ligation of adapters at both extremities of the restriction fragments, and finally, selective PCR amplification of the fragments to generate a fingerprint specific to individuals, varieties, or species (3). It has number of potential applications such as monitoring inheritance of agronomic traits in plant and animal breeding, diagnostics of genetically inherited diseases, pedigree analysis, forensic typing, parentage analysis, screening of DNA markers linked to genetic traits, and microbial typing (4). The AFLP technique has several advantages over other DNA fingerprinting systems. The most important of these are the capacity to examine an entire genome for polymorphism and its reproducibility. Additionally, it can be applied to any DNA samples including human, animal, plant, and microbial DNAs, giving it the potential to become a universal DNA fingerprinting system (4). We argue here that an AFLP-based method, which exploits a pair of enzymes and selective PCR amplification, provides an effective means to evaluate and quantify induced variation by the tissue culture and that the use of an automatic sequencer would increase the capability of processing to analyze high number of samples simultaneously. Several considerations presented here must be taken into account prior to applying such technology in order to obtain the best results and feasible profiles for the analysis.

2. Materials 1. 1.5-mL centrifuge tubes. 2. 0.2/0.5-mL thin-walled centrifuge tubes (depending on thermal cycler). 3. Automatic pipettes capable of dispensing 1–20 mL and 20–200 mL. 4. Autoclaved, aerosol-resistant tips for automatic pipettes. 5. Centrifuge capable of generating a relative centrifugal force of 14,000 × g. 6. 37°C, 65°C, 70°C, 90°C water baths or programmable thermal cycler gradient. 7. Thermal cycling plates and caps. 8. Submerged horizontal electrophoresis system for agarose gels. 9. CEQ 8000 Series genetic analysis system (Beckman) or another system of capillary electrophoresis. 10. Gel documentation system.

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3. Reagents and Solutions 1. DNA isolation: All solutions should be made using double sterile and deionized water. Prepare and store all reagents at room temperature unless otherwise stated. (a) 1 M Tris pH 8: weigh 121.1 g of Tris-Base (FW 121.1) and adjust to 1 L of final volume (see Note 1). (b) 0.5 M EDTA: weigh 186.12 g of EDTA (FW 372.24) and adjust to a final volume of 1 L (see Note 2). (c) 5 M NaCl: weigh 292 g NaCl (FW 58.4) and adjust to a final volume of 1 L. (d) DNA isolation buffer: 100 mM Tris pH 8, 50 mM EDTA, and 500 mM NaCl. (e) 100 mM b-Mercaptoethanol solution: take 700 mL of b-mercaptoethanol (FW 78.13) molecular biology grade and dilute with water to a final volume of 100 mL, in fume hood. (f ) Solution 20% (w/v) sodium dodecyl sulfate (SDS): weigh 20 g of SDS and dilute using hot water to reach 100 mL (see Note 3). The heating before use at 65°C is recommended. (g) 5 M potassium acetate: 245.35 g of potassium acetate (FW 98.14) in 500 mL using water. Once prepared, maintenance at −20°C is recommended. (h) Silicon dioxide 2 g/L (Sigma® Cat. # S5631-500 G): The silicon dioxide (FW 60.09) is prepared in corning tubes of 50 mL, by weighing 2 g of silicon dioxide and diluting to a final volume of 50 mL using water (see Note 4). (i) Ethanol 70% (v/v): mix 70 mL of ethanol (grade molecular biology) in 30 mL of water. Once prepared, maintain at −20°C. 2. Agarose gels. (a) 10× TBE buffer: 0.9 M Tris, 0.9 M boric acid and 20 mM EDTA. Weigh 109 g of Tris-Base (FW121.1), 55.6 g of boric acid and dilute in water. Add 40 mL of 0.5 M EDTA. Adjust to a final volume of 1 L using water. (b) 1× TBE buffer; dilute 100 mL of 10× TBE in 900 mL of water. (c) Agarose gels 1 or 1.5%: weigh 1 or 1.5 g of agarose, respectively, and dissolve in 100 mL of 1× TBE buffer. Boil until agarose is completely dissolved producing a clear

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solution (see Note 5) and to fill the container with the comb according with necessities. (d) Stock of ethidium bromide (EtBr) (10 mg/mL); weigh 50 mg of EtBr (FW 394. 31) and dilute in 5 mL of water (see Note 6). (e) Glycerol-dye bromophenol blue (BPB): 2 mg/mL BPB, 50 mM Tris pH8, 5 mM EDTA, v/v and 25% glycerol; weigh 100 mg of BPB (FW 691.94) and add 2.5 mL of 1 M Tris-base pH 8, 0.5 mL of 0.5 M EDTA, 12.5 mL of glycerol (FW 92.09) and then add water to a final volume of 50 mL and mix well. (f ) Hyper ladder I (BIOLINE® Cat. # H1K5-1006) is a marker for size and mass for DNA display that contain 14 bands in a range of 200–10,000 pb. (g) 100 bp ladder (Invitrogen® Cat. # 15628-019): it consists of 15 fragments between 100 and 1,500 bp in multiples of 100 bp and an additional fragment at 2,072 bp. 3. Double digestion using restriction enzymes (a) Enzymes Eco RI and Mse I (Biolabs Cat # R0101S and Cat # R0525S). Commercially, the concentration is 10 U/mL of each restriction enzyme in a buffer that contain 10 mM Tris–HCl pH 7.5, 50 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 0.1 mg/mL BSA, 50% (v/v) glycerol, 0.1% Triton® X-100. They should be stored at −20°C all the time. (b) 10× NEBuffer 4 for Mse I (Biolabs Cat # B7004S) containing 50 mM potassium acetate, 20 mM Tris–acetate, 10 mM magnesium acetate, 1 mM dithiothreitol, pH 7.9. Store at −20°C (see Note 7). (c) Bovine serum albumin (BSA) (Biolabs Cat # B9001S). 10 mg/mL BSA, 20 mM KPO4, 50 mM NaCl, 0.1 mM EDTA, 5% glycerol, pH 7.0. Store at −20°C. 4. Ligation (a) Annealing buffer: 10 mM Tris, pH 7.5–8.0, 50 mM NaCl, 1 mM EDTA. (b) Double strain Eco RI adapter should be at 5 pmol: To prepare, mix 20 mL of Eco RI adapter-1 (1 nmol/mL, 5¢-CTC GTA GAC TGC GTA CC-3¢) and 20 mL of Eco RI adapter-2 (1 nmol/mL, 5¢AAT TGG TAC GCA GTC TAC3¢) in 20 mL of annealing buffer. Adjust to a final volume of 200 mL and incubate at 65°C for 10 min. Slow cooling to room temperature should take place for 45–60 min. The final concentration of the mixture is 100 pmol. A dilution 1:20 must be prepared by taking

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1 mL of 100 pmol stock solution and diluting up to 19 mL with water. Store at −20°C. (c) Double strain Mse I adapter should be at 50 pmol: To prepare, mix 20 mL of Mse I adapter-1 (1 nmol/mL, 5¢-GAC GAT GAG TCC TGA G-3¢) and 20 mL Mse I adapter-2 (1 nmol/mL, 5¢-TAC TCA GGA CTC AT-3¢) and 20 mL annealing buffer. Adjust to a final volume of 200 mL and incubate at 65°C for 10 min. Slow cooling to room temperature should take 45–60 min. The final concentration of the mixture is 100 pmol/mL. A dilution of 1:2 must be prepared taking 1 mL of 100 pmol stock solution and diluting up to 1 mL with water. Store at −20°C. (d) T4 DNA ligase (Invitrogen Cat # 15224-017): 1 unit/mL in 10 mM Tris–HCl (pH 7.5), 1 mM DTT, 50 mM KCl, 50% glycerol (v/v). Store at −20°C. (e) 5× buffer of T4 DNA ligase: 250 mM Tris–HCl pH 7.6, 50 mM MgCl2, 5 mM ATP, 5 mM DTT, 25% (w/v) polyethylene glycol-8000. Store at −20°C. (f ) TE buffer: 10 mM Tris–HCl (pH 8.0), 0.1 mM EDTA. 5. Primers for AFLPs: AFLP primers consist of three parts: a core sequence, an enzymatic specific sequence (ENZ), and a selective extension (EXT) (3). This is illustrated bellow for Eco RI and Mse I primers with three selective nucleotides (represented by NNN) and they could correspond to any of the sequence described in Table 1: CORE ENZ EXT Eco RI 5-GACTGCGTACC AATTC NNN-3 Mse I 5-GATGAGTCCTGAGTAA NNN-3 6. PCR. Preamplification. For selective preamplification, a specific primer combination of Eco RI and Mse I is used. Both primer Eco RI (5¢-GACTGC GTACCAATTCN-3¢) and primer Mse I (5¢-GACTGCGT ACCAATTCN-3¢) must be prepared at 20 pmol/mL. (a) To prepare a stock solution (100 pmol/mL) of each primer, the stock of 100 pmol/mL it is used to make a 1:5 dilution (take 1 mL of 100 pmoles each stock and dilute 5 mL of water ultrapure). Final concentration of each primer should be 20 pmol/mL. Store at −20°C. (b) 10 mM dNTP (Invitrogen Cat # 18427-013). Mix dATP, dCTP, dGTP, and dTTP (2¢-deoxynucleoside 5¢-triphosphates) at a concentration of 10 mM in Tris–HCl (pH 7.5). Store at −20°C.

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Table 1 AFLP primer combinations. Primer combinations that can be used for different organisms that contain a range of genomic DNA content between 2 and 7 pg per haploid genome. First nucleotides on the primers are A and C for Eco RI and Mse I, respectively, and they are used on the previous preamplification step Mse I selective nucleotides C A A Eco RI selective nucleotides

A

A

C C

G

T

A

G C

G

T

A

T C

G

T

A

C

G

T

A C G T

C

A C G T

G

A C G T

T

A C G T

(c) 10× PCR buffer: 200 mM Tris–HCl (pH 8.4), 500 mM KCl. Store at −20°C. (d) Taq DNA polymerase (Invitrogen Cat # 11615-025): 10 U/mL of Taq DNA polymerase, 20 mM Tris–HCL (pH 8.0), 0.1 mM EDTA, 1 mM DTT, 50% (v/v) glycerol, and stabilizers. Store at −20°C. (e) 50 mM MgCl2. 7. PCR. Selective amplification. (a) Primer Eco RI (5¢-GACTGCGTACCAATTCNNN-3¢) at 2.5 pmol/mL. Prepare a stock solution of 100 pmol/mL, and then take 1 mL of 100 pmoles stock and dilute in 40 mL of water ultrapure.

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(b) Primer Mse I (5¢-GATGAGTCCTGAGTAANNN-3¢) at 6.7 pmol/mL. Prepare a stock of 100 pmol/uL and dilute by taking 1 mL of the stock in 15 mL of water. 8. Fragment analysis (a) DNA size standard kit 400 (Beckman Cat # 608098). Includes DNA fragments of the following sizes labeled with WellRED fluorescent dye: 60, 70, 80, 90, 100, 120, 140, 160, 180, 190, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400, and 420 nucleotides. (b) Separation gel 20 mL for 8800 Series (Beckman Cat # 391438). Linear polyacrylamide (LPA) denaturing gel assures high-resolution separations. (c) Separation buffer (Beckman Cat # 608012). (d) Samples loading solution, SLS (Beckman Cat # 608082). (e) WellRED Dyes-labeled primers.

4. Methods 1. Isolation of DNA: The most critical requirement for an efficient PCR amplification is a high quality DNA which must be free of contaminant compounds that could inhibit the enzymatic reaction catalyzed by the Taq DNA polymerase. Thus, an easy, fast, and efficient protocol for DNA extraction reported by Echevarria-Machado I et al. (5) is suggested for the vast application on several plant species as follows: 500 mg of leaf is chopped into small pieces and placed into a mortar and frozen by adding liquid nitrogen (see Note 8). The powder is transferred to a 2.0-mL Eppendorf tube containing 1 mL of a prewarmed (65°C) DNA isolation buffer containing 100 mL of 100 mM b-mercaptoethanol solution. The suspension must be shaken briefly to obtain a homogeneous suspension. Add 100 mL of SDS 20% and shake it vigorously for several seconds and incubate at 65°C for 10 min. To this, add 500 mL acetate potassium 5 M and shake vigorously for several seconds and incubate on ice for 20 min. The samples must be centrifuged immediately for 5 min at 13,800 × g. The supernatant is transferred to a 1.5-mL Eppendorf tube and 300 mL of silicon dioxide is added and mixed slowly, and centrifuged immediately for 5 min at 13,800 × g (see Note 9). The supernatant is discarded and the pellet washed carefully with 0.5 mL of 70% ethanol for three times, after which a

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Fig. 1. Quality control evaluation by electrophoresis during several steps of the AFLP process. (a) Genomic DNA of several individuals (1–4) of Agave fourcroydes run on 1% agarose gel. (b) Double restriction-ligation of genomic DNA of several individuals on 1% agarose gel. DNA represents a nondigested sample. (c) Preamplification profile of several individuals (1–4) on 1.5% agarose gel. MM corresponds to 1 kb ladder.

spin for 2 min at 900 × g is needed to remove the remaining ethanol (see Note 10). (a) The pellet is air-dried overnight and dissolved in 50 mL of sterile water pH 7.4. (b) The mix must be centrifuged immediately for 5 min at 13,800 × g. The supernatant is transfer carefully into a new 1.5-mL Eppendorf tube (see Note 10). 2. Integrity and concentration of DNA. (a) To check the integrity of the DNA, 5 mL of the solution of DNA are mixed with 2 mL of the glycerol dye BPB and electrophoresed on a 1.0% agarose gel at 80 V for approximately 25 min. A predominant and intense band is expected (see Fig. 1a). (b) The concentration of DNA can be checked by spectrophotometry (with a NanoDrop 1000 spectrophotometer) at 260 nm/280 nm. (c) A dilution of each DNA is prepared at 100 ng/mL, in order to simplify the preparation and dispend of the mixtures for the next steps. 3. Double digestion of DNA using EcoRI and MseI restriction enzymes. (a) Five microliters of genomic DNA (100 ng/mL) must be double digested with 0.4 U EcoRI (10 units/mL), 0.1 U MseI (10 units/mL), in 20 mL final volume that contain 2 mL 10× restriction buffer MseI, 0.2 mL BSA (10 mg/mL), and 12.3 mL H2O (see Note 11). (b) The restriction mixture is incubated for 3 h at 37°C.

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(c) The enzymes must be inactivated by incubation at 65°C for 15 min. (d) The ligation of adapters could be done immediately; otherwise, it is recommended to store the restriction mixture at −20°C up to use. 4. Linker addition. Following to the heat inactivation of the restriction endonucleases, the genomic DNA fragments should be ligated to EcoR I and Mse I adapters to generate a template DNA for amplification based on the recognition by the specific primers to the adapter regions (see Note 12). (a) The restricted DNA is incubated with 10 mL of a mix containing 1.0 mL EcoRI adapter (5 pmol), 1.0 mL MseI adapter (50 pmol), 6.0 ml 5× buffer de T4 DNA ligase, 1.0 U T4 DNA ligase, and 1.0 mL H2O. (b) Mix gently at room temperature and centrifuge briefly to collect contents at the bottom of the tube, and incubate for 16 h at 20°C (heatblock or PCR machine). (c) In order to check the preamplification reaction, aliquots of 5 mL of the preamplification are mixed with 2 mL of glycerol loading dye BPB and loaded into the slots, when the 1.5% agarose gel has been solidified, and the electrophoresis is carried out at 80 V for approximately 15 min. The profile is observed using a UV-transilluminator (Fig. 1b). 5. Preamplification with primers that contain a single selective nucleotide. (a) The ligated DNA from the previous step is diluted 1:10 using TE and then 5 mL of this dilution is used for the preamplification reaction in a mixture that contain 1.0 mL EcoRI primer E01 (20 pmol), 1.0 mL MseI primer M01 (20 pmol), 2.0 mL 10× PCR buffer, 0.4 mL 10 mM dNTPs, 0.6 mL 50 mM MgCl2, 0.1 mL Taq polymerase (5 units/mL), and 9.9 mL H2O to reach 20 mL of final volume. (b) The PCR conditions differed depending on the nature of the selective extensions of the AFLP primers used for amplification. The condition for the PCR include an initial denaturation for 5 min at 94°C, followed by 20 cycles consisting of a denaturation step by 30 s at 94°C, an annealing step for 1 min at 56°C, and an extension step for 1 min at 72°C. A final extension step at 72°C at 7 min is needed. (c) In order to check the preamplification reaction, aliquots of 5 mL of the preamplification are mixed with 2 mL of glycerol loading dye BPB and loaded into the slots, when the 1.5% agarose gel was solidified, and the electrophoresis is

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carried out at 80 V for approximately 15 min. The profile is observed using a UV-transilluminator (see Fig. 1c) (d) To prepare the reaction for selective amplification, dilute 3 mL of the preamplification products in 147 mL H2O (1:50 dilution) (see Note 13) 6. Selective amplification PCR reactions must be prepared within a thin wall microplate or PCR tubes. All reagents should be kept on ice while preparing the PCR reactions. Final concentration of the EcoRI labeled primers in the PCR reaction should be 0.25 mM. The WellREDLabeled primers are designed specifically for use with the CEQ series Genetic 8800 analysis systems and are excited to fluorescence using diode lasers (D2, D3, and D4) (see Note 14). (a) The reaction contain 5 mL of preamplified DNA diluted 1:50, 1.0 mL EcoRI labeled primer + 3, 2.25 mL MseI primer + 3 (6.7 pmol/mL), 0.2 mL 10 mM dNTPs, 1.0 mL 10× PCR-buffer, 0.3 mL 50 mM MgCl2, 0.1 mL Taq DNA polymerase (5 units/mL), and 0.15 mL H2O in 10 mL final volume (see Note 15). (b) AFLP reactions with selective primers were performed with a touchdown program that works well for most primer sets with an initial denaturation step for 5 min at 94°C, followed by 12 cycles with denaturation step for 30 s at 94°C, 30 s for annealing step at 65°C and 1 min extension step at 72°C. In each cycle, a decrease of 0.7°C in the annealing temperature is done. Final annealing temperature reaches 56°C which is used for the next 24 cycles, with final extension step at 72°C for 7 min. (c) For sample preparation, load into the automatic sequencer 0.25–3.0 mL of PCR product added to the SLS–size standard mix. For optimal analysis results, do not saturate the detection system by overloading the sample separation with labeled PCR products. A maximum of three different labeled primers (Different dyes) can be used simultaneously to separate on the sequencer with a prior individual characterization of each profile. (d) For more consistent pipetting, the samples should be diluted in SLS and loaded in a larger volume. For example, for 0.25 mL of the original sample, load 2.5 mL of a 1:10 dilution. (e) The relative signal strengths of the amplification products vary depending on the dye label. As a guide, roughly equal signal strengths can be obtained by adding the following relative volumes of PCR reaction products: 0.1 mL D4 PCR reaction, 0.2 mL D3 PCR reactions, and 0.4 mL D2 PCR reactions. Dilute the reactions appropriately to

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increase pipetting accuracy. If large volumes of diluted reactions are used, compensate to reach a final injection volume of approximately 40 mL. (f ) The amount of PCR product used will depend upon the efficiency of the PCR reaction. The volumes given above are a recommended starting point. (g) Fill each well of one row of the sample plate with 25 mL of the prepared test sample/size standards mix. (h) Add one drop of mineral oil to each of the 8 wells and load onto the instrument. (i) Run the prepared sample on the instrument using the “FragTest” or Frag-1 and Frag-3 run method. Several different separation methods and analysis parameter sets are provided with the System. The Frag-1 and Frag-3 separation methods are appropriate for use with the size standard 400 ladder. Once the un in over, it is necessary to verify that the six peaks of the Fragment Analysis Test Sample have been identified and their sizes estimated, as listed above. The Size Standard-400 contains fragments of the following sizes, labeled with D1 (red) dye: 60, 70, 80, 90, 100, 120, 140, 160, 180,190, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400, and 420 nucleotides. (j) To analyze the profiles (Fig. 2), a binary matrix (1 = band present, 0 = band absent) is prepared based on the pattern of AFLP bands. A polymorphic band is defined as a band (Pick) that is absent from at least one individual. Genetic similarity index (GSI) could be determined according to Nei and Li (6). The resulting dendrogram could be obtained using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), using the SAHN (Sequential

Fig. 2. AFLP profiles of A. angustifolia using two primer combinations in an automatic sequencer. Several primer combination produce different fingerprint profiles.

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Agglomerative Hierarchical Nested Cluster Analysis) statistical module of NTSYS (Numerical Taxonomy and Multivariate Analysis System) software version 2.02.

5. Notes 1. To adjust the pH use concentrated HCl (12 M) when around pH 8 if you prefer adjusted with series of the 6 N or 1 N HCl. The concentrate HCl is toxic and dangerous for the environment. For manipulation use face shields, full-face respirator, gloves, goggles, multipurpose combination respirator cartridge. Before use, check the risk and safety statements. 2. To prepare EDTA, it is necessary to adjust to pH 8 in order to increase the solubility; add gradually the reactant to avoid lumps. Use NaOH 1 N to adjust pH. 3. Prewarm water up to 65°C and add gradually, and shaking gently to prevent foaming. For manipulation, use eye shields, face shields, mask, gloves. Before use check the risk and safety statement. 4. Before use, it is necessary to remove small particles of silica (to prevent DNA lost) by washing for at least three times, mixing the solution with 500 mL of water and shaking and after that centrifuging at 17,000 × g for 5 min and discarding supernatant. Repeat the process until the supernatant appears clear. 5. It is possible to use a microwave oven; to avoid air bubbles, turn off the microwave immediately after boil. Wait for it to cool before discarding into the mold, avoiding bubbles. 6. Ethidium bromide intercalates double-stranded DNA and RNA and acts as a mutagen. EtBr is toxic for use. Utilize eye shields, face shields, mask, and gloves. It is important to designate a special area and management to work with the materials containing EtBr. Check the risk and safety statement. 7. The use of 10× NEBuffer 4 Mse I guarantees a cutting efficiency of 100% for the enzyme Mse I and Eco RI at 37°C. 8. The tissue should not be thawed during the process. It is necessary to add liquid nitrogen several times. 9. Mix by inversion or vortex the silicon dioxide until the pellet disappears. 10. Without removing the tubes from silicon dioxide, carefully aspirate and discard the supernatant without disturbing the pellet by angling the pipette such that the tip is pointed away from the pellet.

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11. The AFLP technique is based on the amplification of subsets of genomic restriction fragments using PCR. DNA is cut with restriction enzymes, and double-stranded (ds) adapters are ligated to the ends of the DNA fragments to generate template DNA for amplification. The sequence of the adapters and the adjacent restriction site serve as primer binding sites for subsequent amplification of the restriction fragments. Selective nucleotides are included at the 3¢ ends of the PCR primers, which therefore can only prime DNA synthesis from a subset of the restriction sites. Only restriction fragments in which the nucleotides flanking the restriction site match the selective nucleotides will be amplified (3). 12. Depending on the intensity of the amplified fragments, the dilution will be at 1:5 or 1:10. 13. Depending on the intensity of the amplified fragments, the dilution will be at 1:25 or 1:50 14. Storage of all Fragment Analysis reagents (Size Standards, Test Sample, and Mobility Calibration Standard) must be in a −20°C non-frost-free freezer. Certain primers may work better at higher or lower concentrations because of primer sequence specific factors. It is recommended to start at 0.025 mM for the System, and adjust as required. 15. The most important factor in determining the number of restriction fragments amplified in a single AFLP reaction is the number of selective nucleotides in the selective primers (Fig. 2). The selective primers in the AFLP are three selective nucleotides used with plants having genomes ranging in size from 5 × 108 to 6 × 109 bp; the number of fragments amplified per sample per primer pair averages 50, but may range from as low as 10 to ~100 depending on the sequence context of the selective nucleotides, and the complexity of the genome (7, 8).

Acknowledgments The authors thank CONACyT for the financial support (project: 50268) to apply this technique on several species of agaves, and M.C. Miriam Monforte-González for the academic support in regard to the art illustrations of this paper.

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References 1. Larkin PJ, Scowcroft WR (1981) Somaclonal variation—a novel source of variability from cell cultures for plant improvement. Theor Appl Genet 60:197–214 2. Duncan RR (1997) Tissue culture-induced variation and crop improvement. Adv Agron 58: 201–240 3. Vos P et al (1995) AFLP: a new concept for DNA fingerprinting. Nucleic Acids Res 23:4407–4414 4. Bears MJ et al (1998) Amplified fragment length polymorphis (AFLP): a review of the procedure and its applications. J Ind Microbiol Biotechnol 21:99–114

5. Echevarria-Machado I et al (2005) A simple and efficient method for isolation of DNA in high mucilagenous plant tissues. Mol Biotechnol 31:129–135 6. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76: 5269–5273 7. Zabeau M, Vos P (1993) European patent application number EP 0534858 8. Lin JJ, Ku J (1995) AFLP: a novel PCR-based assay for plant and bacterial fingerprinting. Focus 17:66

Chapter 27 Biolistic- and Agrobacterium-Mediated Transformation Protocols for Wheat Cecília Tamás-Nyitrai, Huw D. Jones, and László Tamás Abstract After rice, wheat is considered to be the most important world food crop, and the demand for high-quality wheat flour is increasing. Although there are no GM varieties currently grown, wheat is an important target for biotechnology, and we anticipate that GM wheat will be commercially available in 10–15 years. In this chapter, we summarize the main features and challenges of wheat transformation and then describe detailed protocols for the production of transgenic wheat plants both by biolistic and Agrobacteriummediated DNA-delivery. Although these methods are used mainly for bread wheat (Triticum aestivum L.), they can also be successfully applied, with slight modifications, to tetraploid durum wheat (T. turgidum L. var. durum). The appropriate size and developmental stage of explants (immature embryo-derived scutella), the conditions to produce embryogenic callus tissues, and the methods to regenerate transgenic plants under increasing selection pressure are provided in the protocol. To illustrate the application of herbicide selection system, we have chosen to describe the use of the plasmid pAHC25 for biolistic transformation, while for Agrobacterium-mediated transformation the binary vector pAL156 (incorporating both the bar gene and the uidA gene) has been chosen. Beside the step-by-step methodology for obtaining stably transformed and normal fertile plants, procedures for screening and testing transgenic wheat plants are also discussed. Key words: Agrobacterium, Biolistics, Cereals, Embryogenic cultures, Genetic transformation, Triticum aestivum L., Wheat

1. Introduction Wheat forms the staple food of the human diet in over 60 countries and provides 10–20% of the daily calorific intake for almost half the world’s population. Wheat flour is unique in its ability to be processed and baked into leavened bread, but it is also a major constituent of many other foods including biscuits, cakes, breakfast cereal, pasta, and noodles. In addition, low-grade wheat and industrial

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_27, © Springer Science+Business Media, LLC 2012

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wheat by-products are incorporated into animal feed products and industrial products such as inks, paper, textiles, and pharmaceuticals, among others. Wheat became the last cereal crop to be successfully genetically transformed in 1992 (1), and aspects of this technology have been reviewed previously (2–11). The transformation of elite or model wheat genotypes provided the opportunity to study the role of specific gene sequences in wheat and to introduce important agronomic traits into different varieties. Agronomically important properties such as resistance to biotic (pests, pathogens) and abiotic (drought, soil salinity, heat or cold) stresses have been investigated (12–16). In addition, this technique was successfully used for the modification of the end-use quality of several wheat varieties by increasing dough strength, focusing on one specific group of polymeric gluten proteins, called high-molecular-weight glutenin subunits (HMW-GS) (17–25). Field trials revealed no differences between the transgenic and control lines in terms of relative stability of expression of the endogenous and transgenic forms of the HMW subunit genes and inheritance between generations at several locations (23, 26–29). The effects of another storage protein, the low-molecular-weight glutenin subunit (LMW-GS), on the dough quality were also studied in transgenic wheat lines, and it was also demonstrated that transgenic approach could be used to fine-tune the properties of wheat lines for different end-use purposes (30–32). Improvements to the nutritional quality of the wheat flour and dough were also seen as relevant goals for the overall sustainability of wheat as a food crop (reviewed by Shewry and Zhu et al. (33, 34)). Wheat whole grain contains several important vitamins, minerals, a high amount of fibre, complex carbohydrates, and a substantial amount of proteins, but in the white flour some of these components are lost due to the milling process. To improve indices of large-bowel health in rats, Regina et al. (35) generated highamylose wheat by RNA interference. To improve the nutritional quality of the wheat flour and the dough, Tamas et al. (36) expressed an amarant albumin (Ama1) gene in transgenic wheat endosperm increasing the content of some essential amino acids (tyrosine, threonine, and lysine) between 3.8 and 7.3% in the flour. To modify the protein content and quality attributes of the endosperm, it requires tissue specific promoters that underline all the efforts carried out to characterize storage protein promoters and improve their strength to enhance the recombinant protein yield in the transgenic wheat grain (37–40). Wheat was also used to study if the endosperm tissue can be considered as a seed based production platform of pharmaceuticals, expressing medically important antibodies, after the introduction of the appropriate genes into the genome (41). The success in the plant biopharmaceutical production and molecular farming

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efforts may have more of an impact on the social acceptance of the GM technology. The protocols described below are adapted from reliable and widely used methods of wheat transformation (4, 36, 42–44) and have been augmented by a Note section (Subheading 4) explaining our detailed experiences in generating viable and stable transgenic lines. Regardless of the DNA-delivery methods and specific regeneration methods, the herbicide selection system, based on the bar gene and the phosphinothricin (PPT) selection agent, was applied to distinguish between transgenic and non-transgenic cell lines. For particle bombardment, the plasmid construct pAHC25 (45) was used, carrying the selectable marker gene (bar) and the reporter gene (uidA) both under the control of the constitutive ubiquitin promoter (Ubi1) from maize. The Agrobacterium-mediated transformation exploited the Agrobacterium tumefaciens strain AGL1 (46). This super-virulent strain contains the plasmids pAL154/ pAL156 based on the plasmid pSoup/pGreen (47). The single T-DNA in binary vector pAL156 incorporates the bar gene and a modified uidA gene with an intron within the open reading frame to prevent its expression in A. tumefaciens itself; both genes are driven by the promoter of the maize ubiquitin gene plus the first intron of it (45). The bar gene is located next to the left border, and uidA gene is adjacent to the right border. The plasmid pAL154 helps the replication functions for pAL156 in trans and contains the 15 kb Komari fragment (48, 49) supplying extra vir genes. The following Methods section (Subheading 3) is divided into three sections: the first covers tissue culture conditions and media composition, the second covers selection and growth of healthy, fertile transgenic plants, and the third section describes the screening of T0 lines at molecular level by PCR and provides methods to measure the enzyme activity of the reporter and selectable marker genes. The action of β-glucuronidase enzyme, encoded by the uidA gene, is demonstrated in a non-quantified way by histochemical GUS staining, while the activity can be quantified using the MUG fluorescent assay. The bar gene expression is demonstrated either by herbicide leaf painting or using the ammonium assay to determine the activity of phosphinothricin acetyltransferase (PAT) enzyme.

2. Materials 2.1. Materials for Biolistics Transformation 2.1.1. Plant Materials

Wheat (Triticum aestivum L.) plants (cv. Cadenza, Fielder, Florida, and different elite varieties) and tetraploid durum wheat (T. turgidum L. var. durum) are grown under controlled conditions in temperature growth rooms or phytotron chambers. Artificial light is provided by banks of HQI lamps 400 W (Osram Ltd., UK) in

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growth rooms [intensity ~ 700 μmol/m2 s photosynthetically active radiation (PAR) for a 16-h photoperiod, and the day–night temperature regime is 18/14°C). Prior to transfer to these conditions, winter wheat seeds are imbibed and vernalized for 6 weeks at 4°C. To ensure continuous production of immature embryos, batches of seeds are planted every 1 or 2 weeks. Particular care should be given to maintain growing conditions at the same level (see Note 1). 2.1.2. Sterilization Materials for Wheat Spikes and Caryopses

1. 70% (v/v) aqueous ethanol. 2. Sodium hypochlorite (NaOCl, 1.3%) aqueous solution with a drop of surfactant (Triton X-100 or Tween-20) (see Note 2). 3. Sterile distilled water (reverse osmosis, purity of 18.2 MΩ/cm).

2.1.3. Stock Solutions for Tissue Culture Media

The final tissue culture media (Subheading 2.1.4) are prepared from stock solutions detailed below. Prepare all solutions using ultrapure water (purity of 18.2 MΩ/cm) and analytical grade reagents. 1. Ferrous sulphate chelate solution (100×): buy a ready-to-use solution (Sigma-Aldrich) or dissolve 3.725 g/L EDTANa2.2H2O (ethylenediaminetetraacetate disodium salt) and 2.785 g/L FeSO4.7H2O (see Note 3). Autoclave at 121°C for 20 min, store at 4°C for maximum 2 months. 2. MS macrosalts (10×): 16.5 g/L NH4NO3, 19.0 g/L KNO3, 1.7 g/L KH2PO4, 3.7 g/L MgSO4.7H2O, 4.4 g/L CaCl2.2H2O (see Note 3). Autoclave at 121°C for 20 min, store at 4°C for maximum 2 months. 3. MS Vitamins (-glycine) (1,000×): 100 mg/L thiamine·HCl, 500 mg/L pyridoxine·HCl, 500 mg/L nicotinic acid. Prepare 100 mL at a time (see Note 3), filter-sterilize (see Note 4), and store at 4°C for maximum 2 months. 4. L7 macrosalts (10×): 2.5 g/L NH4NO3, 15.0 g/L KNO3, 2.0 g/L KH2PO4, 3.5 g/L MgSO4.7H2O, 4.5 g/L CaCl2.2H2O (see Note 3). Autoclave at 121°C for 20 min and store at 4°C for maximum 2 months. 5. L7 microsalts (1,000×): 15.0 g/L MnSO4 (various hydrated states alter the required weight), 5.0 g/L H3BO3, 7.5 g/L ZnSO4.7H2O, 0.75 g/L KI, 0.25 g/L Na2MoO4.2H2O, 0.025 g/L CuSO4.5H2O, 0.025 g/L CoCl2.6H2O. Prepare 100 mL at a time (see Note 3), filter-sterilize (see Note 4), and store at 4°C for maximum 2 months. 6. Silver nitrate (AgNO3) solution (used to promote embryogenesis): 20 mg/mL in water. Prepare 10 mL at a time in graduated plastic tube. Mix well, filter-sterilize (see Note 4), and aliquot into 1 mL volumes. Store at −20°C in the dark

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(see Note 5). Should remain effective for at least a year, provided no freezing–thawing has occurred. 7. Copper sulphate (CuSO4) solution: 0.1 M (16 mg/mL) (24.97 g CuSO4.5H2O/L) in water. Prepare 10 mL at a time in graduated plastic tube. Mix well, filter-sterilize (see Note 4), and store at 4°C in 1 mL aliquots for maximum 2 months. 8. L7 vitamins/inositol (200×): 40.0 g/L myo-inositol, 2.0 g/L thiamine·HCl, 0.2 g/L pyridoxine·HCl, 0.2 g/L nicotinic acid, 0.2 g/L Ca-pantothenate, 0.2 g/L ascorbic acid. Prepare 100 mL at a time (see Note 3). Filter-sterilize (see Note 4) and store at −20°C in 10 mL aliquots (should remain effective for at least a year). 9. Amino acids 3AA (25×): 18.75 g/L glutamine, 3.75 g/L proline, 2.5 g/L asparagine. Prepare 200 mL at a time (see Note 3). Store solution at −20°C in 40 mL aliquots (should remain effective for at least a year). 10. 2,4-dichlorophenoxyacetic acid (2,4-D) (auxin type hormone): 1 mg/mL in ethanol/water. Dissolve 10 mg powder in 2 mL ethanol in graduated plastic tube and then add water to volume of 10 mL. Mix well, filter-sterilize (see Note 4) and store at −20°C in 1 mL aliquots (should remain effective for at least a year). 11. Zeatin mixed isomers (cytokinin type hormone): 10 mg/mL in HCl/water. Dissolve 100 mg powder in 3 mL 1 M HCl in graduated plastic tube and then add water to volume of 10 mL. Mix/vortex well, filter-sterilize (see Note 4) and store at −20°C in 1 mL aliquots (should remain effective for at least a year). 12. PPT (synthetic l-phosphinothricin) selection agent: 10 mg/mL in water (see Note 6). Prepare 10 mL at a time in a graduated plastic tube. Mix/vortex well, filter-sterilize (see Note 4), and store at −20°C in 1 mL aliquots (should remain effective for at least a year). 13. Agargel (2×): 10 g/L in water. Add 4 g gel powder to 400 mL water in a 500-mL bottle and sterilize it at 121°C for 20 min in an autoclave. Shake well both before and after autoclaving to avoid non-uniform solidification which leads to difficulties when re-melting. Store at room temperature and melt in microwave before use. 2.1.4. Tissue Culture Media for Wheat Immature Scutella Callus Induction Media

Tissue culture media are prepared at double strength to allow the addition of an equal volume of double-strength gelling agent (Agargel) melted (see Notes 7–9). 1. Callus Induction Media (CI/Biol) (2×): 20 mL/L ferrous sulphate chelate solution (see Note 7), 200 mL/L MS macrosalts, 2 mL/L L7 microsalts, 2 mL/L MS (-glycine) vitamins,

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200 mg/L myo-inositol, 40 mL/L 3AA amino acids, 180 g/L (9% final concentration) sucrose (see Note 10). Adjust pH to 5.8 with 5 M NaOH or KOH and filter-sterilize (see Note 4). Prepare in 400 mL volumes (see Notes 3 and 8) and store at 4°C for maximum 2 months. 2. CI/Biol: Mix an equal volume of CI/Biol (2×) with sterile, melted Agargel (see Note 9). Add 0.5 mg/L 2,4-D, 10 mg/L AgNO3, mix by rotating the bottle gently, and pour into 9 cm diameter Petri dishes (26–30 mL per dish). Store at 4°C in the dark (see Note 5) for maximum 3 weeks. Regeneration Media

1. R (2×): 20 mL/L ferrous sulphate chelate solution (see Note 7), 200 mL/L L7 macrosalts, 2 mL/L L7 microsalts, 10 mL/L L7 vitamins/inositol, 60 g/L maltose. Adjust pH to 5.8 with 5 M NaOH or KOH and filter-sterilize (see Note 4). Prepare in 400 mL volumes (see Notes 3 and 8) and store at 4°C for maximum 2 months. 2. RZD + 1/2Cu (for stage 1. regeneration without selection): mix an equal volume of R (2×) medium with sterile, melted Agargel (see Note 9). Add 5 mg/L zeatin, 0.1 mg/L 2,4-D, and 0.05 mM (8 mg/L) CuSO4, mix by rotating the bottle gently, and pour into 9-cm Petri dishes (26–30 mL per dish). Store at 4°C for maximum 3 weeks. 3. RZ (for controls at stage 2. regeneration): mix an equal volume R (2×) with sterile, melted Agargel (see Note 9). Add 5 mg/L zeatin, mix by rotating the bottle gently, and pour into 9-cm Petri dishes (26–30 mL per dish). Store at 4°C for maximum 3 weeks. 4. R0 (for controls at stage 3. regeneration and for root regeneration): mix an equal volume R (2×) with sterile, melted Agargel (see Note 9). Pour into 9-cm Petri dishes (26–30 mL per dish) or GA-7 Magenta vessels (Sigma-Aldrich) (55–60 mL per vessel). Store at 4°C for maximum 3 weeks.

Selection Media

1. RZPPT2-3 (for stage 2. regeneration with selection): mix an equal volume of R (2×) with sterile, melted Agargel (see Note 9). Add 5 mg/L zeatin and 2–3 mg/L PPT (see Note 11). Mix by rotating the bottle gently and pour into 9-cm Petri dishes (26–30 mL per dish). Store at 4°C for maximum 3 weeks. 2. RPPT3-4 (for stage 3. regeneration and for root regeneration with selection): mix an equal volume of R (2×) with sterile, melted Agargel (see Note 9). Add 3–4 mg/L PPT (see Note 11). Mix by rotating the bottle gently and pour into 9-cm Petri dishes (26–30 mL per dish) or GA-7 Magenta vessels (55–60 mL per vessel). Store at 4°C for maximum 3 weeks.

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2.1.5. Materials and Consumables for Bombardment

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1. 3 M Calcium chloride: dissolve 4.40 g CaCl2.2H2O in 10 mL water. Mix/vortex well. Filter-sterilize (see Note 4) and store at −20°C in 50 μL aliquots (should remain effective for at least a year). 2. 0.1 M spermidine free-base: prepare 1 mL of 1 M stock solution from powder in sterile ultrapure water and store at −80°C in 20 μL aliquots. Prepare the 0.1 M working solution by dilution of stock in sterile ultrapure water under sterile conditions. Mix/vortex well and store at −20°C in 10 μL and 20 μL aliquots for 6 and 12 shots, respectively. If once thawed, it should not be used again. 3. Gold particles: 0.6 μm (sub-micron) gold particles (Bio-Rad Laboratories) as the smaller, more uniform size of the particles is preferable for small wheat cells. For gold suspension (40 mg/mL) preparation see Subheading 3.1.3. 4. Macrocarriers, stopping screens, 650 or 900 psi rupture discs (all Bio-Rad Laboratories). 5. Plasmid DNA: prepare high purity DNA sample, using for example Qiagen kit (Qiagen Ltd.), adjust the concentration to 1 μ(m)g/μ(m)L in sterile TE buffer (10 mM Tris–HCl and 1 mM EDTA, pH 8.0) and store at −20°C in 20 μL aliquots.

2.2. Materials for AgrobacteriumMediated Transformation 2.2.1. Plant Material and Sterilization Chemicals for Wheat Spikes and Caryopses 2.2.2. Growing A. tumefaciens

2.2.3. Stock Solutions for Tissue Culture Media

1. Plant material: as described in Subheading 2.1.1 for biolistic transformation. 2. Sterilization materials for wheat spikes and caryopses: as described in items 1–3 in Subheading 2.1.2 for biolistic transformation.

1. Standard glycerol inoculum of A. tumefaciens strain AGL1. 2. MG/L medium according to (50): Dissolve 5 g/L mannitol, 1 g/L L-glutamic acid, 250 mg/L KH2PO4, 100 mg/L NaCl, 100 mg/L MgSO4·7H2O, 5 g/L tryptone, and 2.5 g/L yeast extract in ultrapure water (see Note 3). Adjust pH to 7.0 with 5 M NaOH or KOH. Autoclave at 121°C for 20 min. At room temperature add 1 μg biotin (100 μL from sterile stock solution at 1 mg/100 mL) to 1 L medium. Store at 4°C in 10 mL aliquots for maximum 2 months. The final tissue culture media (Subheading 2.2.4) are prepared from stock solutions as it is given in details below. Prepare all solutions using ultrapure water (purity of 18.2 MΩ/cm) and analytical grade reagents.

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1. Ferrous sulphate chelate solution (100×): as described in item 1 in Subheading 2.1.3 for biolistic transformation. 2. MS macrosalts (10×): as described in item 2 in Subheading 2.1.3 for biolistic transformation. 3. L7 microsalts (1,000×): as described in item 5 in Subheading 2.1.3 for biolistic transformation. 4. MS vitamins (-glycine) (1,000×): as described for biolistic transformation in item 3 in Subheading 2.1.3. 5. L7 vitamins/inositol (200×): as described in item 8 in Subheading 2.1.3 for biolistic transformation. 6. Acetosyringone (3¢,5¢-dimethoxy-4¢-hydroxyacetophenone): 10 mg/mL (50 mM) stock solution in 70% ethanol. Prepare 10 mL at a time in graduated plastic tube. Mix well, and store at −20°C in 500 μL aliquots (should remain effective for at least a year), or prepare fresh. 7. 2,4-dichlorophenoxyacetic acid (2,4-D) (auxin type hormone): as described in item 10 in Subheading 2.1.3 for biolistic transformation. 8. Zeatin mixed isomers (cytokinin type hormone): as described in item 11 in Subheading 2.1.3 for biolistic transformation. 9. Picloram (plant cell culture tested): 1 mg/mL in ultrapure water. Prepare 10 mL at a time in a graduated plastic tube. Mix well, filter-sterilize (see Note 4), and store at −20°C in 2 mL aliquots (should remain effective for at least a year). 10. Timentin antibiotic (15:1 ratio of ticarcillin disodium and clavulanate potassium): 300 mg/mL in ultrapure water. Prepare 10 mL at a time in a graduated plastic tube. Mix well, filtersterilize (see Note 4), and store at −20°C in 1 mL aliquots (should remain effective for at least a year). 11. PPT selection agent: as described in item 12 in Subheading 2.1.3 for biolistic transformation. 12. Silwet L-77 (Lehle seeds, USA), a 100% non-ionic surfactant: prepare 1% (v/v) solution in water. Filter-sterilize (see Note 4) and store at 4°C in 0.5 mL aliquots. 13. Phytagel (2×): 4 g/L in water. Add 1.6 g gel powder to 400 mL water in a 500-mL bottle and sterilize it at 121°C for 20 min in an autoclave. Shake well both before and after autoclaving to avoid non-uniform solidification which leads to difficulties when re-melting. Store at room temperature and melt in microwave before use. 14. Agargel (2×): as described in item 13 in Subheading 2.1.3 for biolistic transformation.

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2.2.4. Media for Plant Tissue Culture

Inoculation Media

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Tissue culture media are prepared at double strength to allow the addition of an equal volume of gelling agent at double strength (see items 13 and 14 in Subheading 2.2.3) melted (see Notes 7–9). Phytagel is used for inoculation and induction media, while Agargel is used for regeneration- and selection media (R/inDTZ, R/inT, and R/inT-DTT) (see below in this Subheading). 1. Double-strength inoculation medium (IM×2): 20 mL/L ferrous sulphate chelate solution (see Note 7), 200 mL/L MS macrosalts, 2 mL/L L7 microsalts, 2 mL/L MS (-glycine) vitamins, 200 mg/L myo-inositol, 1 g/L glutamine, 200 mg/L casein hydrolysate, 3.9 g/L MES monohydrate buffering agent, 20 g/L glucose, 80 g/L maltose. Adjust pH to 5.8 with 5 M NaOH or KOH and then filter-sterilize (see Note 4). Prepare in 400 mL volumes (see Notes 3 and 8), and store at 4°C for maximum 2 months. 2. Single-strength liquid inoculation medium (for re-suspending Agrobacterium cells in step 3 in Subheading 3.2.2): mix double strength inoculation medium with same volume of sterile, ultrapure water. 3. Semi-solid inoculation medium: mix an equal volume of double-strength inoculation medium with sterile, melted Phytagel (see Note 9). Add 2.0 mg/L 2,4-D, 2.0 mg/L picloram, 200 μM (or 400 μM, see Note 31) acetosyringone, mix by rotating the bottle gently and pour into 5.5 or 9 cm Petri dishes (26–30 mL per dish). Store at 4°C for maximum 3 weeks.

Callus Induction Media

1. Callus Induction Media (CI/Agr) (2×): 20 mL/L ferrous sulphate chelate solution (see Note 7), 200 mL/L MS macrosalts, 2 mL/L L7 microsalts, 2 mL/L MS (-glycine) vitamins, 200 mg/L myo-inositol, 1 g/L glutamine, 200 mg/L casein hydrolysate, 3.9 g/L MES monohydrate, 80 g/L maltose. Adjust pH to 5.8 with 5 M NaOH or KOH and then filtersterilize (see Note 4). Prepare in 400 mL volumes (see Notes 3 and 8), and store at 4°C for maximum 2 months. 2. Semi-solid CI/Agr: mix an equal volume of double-strength induction medium with sterile, melted Phytagel (see Note 9). Add 0.5 mg/L 2,4-D, 2.0 mg/L picloram, 150 mg/L timentin, mix by rotating the bottle gently, and pour into 9 cm Petri dishes (26–30 mL per dish). Store at 4°C for maximum 3 weeks.

Regeneration Media

1. R/in (2×): 20 mL/L ferrous sulphate chelate solution (see Note 7), 200 mL/L MS macrosalts, 2 mL/L L7 microsalts, 10 mL/L L7 vitamins/inositol, 200 mg/L myo-inositol, 60 g/L maltose. Adjust pH to 5.7 with 5 M NaOH or KOH

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and then filter-sterilize (see Note 4). Prepare in 400 mL volumes (see Notes 3 and 8), and store at 4°C for maximum 2 months. 2. R/inDTZ (for stage 1. regeneration without selection): mix an equal volume of double-strength R/in medium with sterile, melted Agargel (see Note 9). Add 0.1 mg/L 2,4-D, 150 mg/L timentin, 5 mg/L zeatin, mix by rotating the bottle gently, and pour into 9 cm Petri dishes (26–30 mL per dish). Store at 4°C for maximum 3 weeks. 3. R/inT (for controls at stage 2–3. regeneration and for strengthening root system): mix an equal volume of double-strength R/in medium with sterile, melted Agargel (see Note 9). Add 150 mg/L timentin, mix by rotating the bottle gently, and pour into 9 cm Petri dishes (26–30 mL per dish) or GA-7 Magenta vessels (55–60 mL per vessel). Store at 4°C for maximum 3 weeks. Selection Media

2.3. Materials for Testing Transient and Stable Gene Expression

2.3.1. Screening the Primary Regenerated Plantlets by PCR

1. R/inT-PPT (for stage 2–3. regeneration and for root regeneration with selection): mix an equal volume of double-strength R/in medium with sterile, melted Agargel (see Note 9). Add 150 mg/L timentin, 2–4 mg/L PPT (see Note 11), mix by rotating the bottle gently, and pour into 9 cm Petri dishes (26–30 mL per dish) or GA-7 Magenta vessels (55–60 mL per vessel). Store at 4°C for maximum 3 weeks. In the following subsections (Subheadings 2.3.1–2.3.3) the materials for detecting the bar and the uidA genes are provided because for biolistic transformation the plasmid constructs pAHC25 (see Note 12), while for the Agrobacterium-mediated transformation the binary vector pAL156 (both incorporating the bar gene and the uidA gene) were applied. 1. DNA extraction reagents and equipment (see Note 14). 2. PCR (polymerase chain reaction) and electrophoresis solutions and equipment. 3. Primers (see Subheading 3.3.1).

2.3.2. Histochemical GUS Assay for Transient and Stable Gene Expression

GUS assay can be conducted in transgenic plants since both the plasmid construct pAHC25 and the binary vector pAL156 in A. tumefaciens strain AGL1 contain not only the selectable marker gene bar but the uidA reporter gene as well (see Notes 12 and 13). 1. X-Glca (5-bromo-4-chloro-3-indolyl-β-D-galacturonide) (or X-Gluc, 5-bromo-4-chloro-3-indolyl-β-D-glucuronide) stock solution (50×): 1 mg/mL (100 mM) in N,N-dimethylformamide (DMF). Prepare 10 mL at a time in graduated plastic tube.

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2. X-Glca (or X-Gluc) working solution: 100 mM phosphate buffer (pH 7.0), 10 mM EDTA, 0.8 mM potassium ferricyanide, 0.8 mM potassium ferrocyanide, 0.1% (v/v) Triton X-100, and 2 mM X-Glca in ultrapure water. Prepare 10 mL at a time in graduated plastic tube from stock solutions (1 M phosphate buffer, 100 mM EDTA, 40 mM potassium ferri- and ferrocyanide, 1% Triton X-100, and 100 mM X-Glca or X-Gluc). Filtersterilize and store in 2 mL aliquots at −20°C. 3. 25-multiwell microtitre plates. 2.3.3. Materials for Analysis of Stable Expression of the bar Gene 2.3.3.1. Leaf Painting Bioassay

The bar gene encodes the enzyme phosphinothricin acetyltransferase (PAT) which confers resistance to phosphinothricin (PPT) and glufosinate ammonium-based herbicides. 1. 0.1% (v/v) Tween-20 solution. 2. Glufosinate ammonium-based herbicide solutions containing 0.2 g/L and 2 g/L PPT (see Note 6). 3. Ballpoint pen and cotton buds.

2.3.3.2. Ammonium Test

1. Ammonium assay incubation medium: 50 mM potassiumphosphate buffer pH 5.8, 2% sucrose, 1.0 mg/L 2,4-D, 25 mg/L glufosinate ammonium, and 0.1% (v/v) Tween-20. 2. Ammonium assay Reagent 1: 34 g/L sodium salicylate, 25 g/L trisodium citrate, 25 g/L sodium tartrate, and 0.12 g/L sodium nitroprusside (see Note 15). Store at 4°C in the dark. 3. Ammonium assay Reagent 2: 30 g/L sodium hydroxide and 0.52 g/L sodium dichloroisocyanurate (see Note 16). Store at 4°C for maximum 2 months. 4. Ammonium chloride: 1 g/L (1,000 mg/L) in ultrapure water. Prepare 100 mL at a time. For 10 mL working solutions (2, 4, 6, 8, and 10 mg/L) pipette 20, 40, 60, 80, and 100 μL, respectively, from the stock into 10 mL ultrapure water in plastic tubes.

2.3.3.3. Herbicide Resistance (PAT) Assay by Spraying Putative Transgenic Plants

1. Glufosinate ammonium-based herbicide solution containing 0.1% (m/v), 1 g/L PPT (see Note 6). 2. Spraying bottle with a volume of 1 or 2 L.

3. Methods 3.1. Method for Biolistic Transformation

This is an optimized method for transformation of immature scutella, but immature inflorescences can also be used as explants (51–54). Carry out all procedures at room temperature unless otherwise specified.

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Fig. 1. Immature embryos prepared from caryopses at 12–16 days post anthesis. The embryos with slightly translucent scutellum and axis turning opaque (No 3) are generally most responsive. The size of the scutella is 0.8–1.2 mm in length; however, genotypic variations can be observed. Smaller and/or larger embryos may respond but with lower efficiencies. White bar represents 1 mm (The photo was taken by Terese Richardson and used with her kind permission). 3.1.1. Collection and Sterilization of Wheat Caryopses

1. Collect spikes from phytotron chambers-grown plants at around 11–12 weeks after sowing (see Subheading 2.1.1 for growing condition). Embryos at the correct stage are usually found 12–14 days post anthesis (DPA). A few grains can be checked at the time of collection to determine the size of the embryos within them (for proper size see step 1 in Subheading 3.1.2 and Fig. 1). 2. Sterilize spikes by rinsing in 70% (v/v) aqueous ethanol for 30 s before removing the immature grains from the panicles. Collect caryopses only from the middle half of each spike and avoid using the inner caryopses of the spikelet that generally contain smaller embryos due to asynchronous development. 3. Surface sterilize the caryopses by soaking them for 15–20 min in sodium hypochlorite (1.3%) aqueous solution with a drop of surfactant (see Note 2) while shaking gently on a platform shaker (~60 rpm). 4. Rinse in sterile distilled water at least three times under aseptic conditions. Maintain the sterile caryopses in moist conditions, but do not keep immersed in water.

3.1.2. Isolation and Pre-culture of Immature Scutella

1. Isolate the embryos microscopically in a sterile environment while removing the embryo axis with a sharp scalpel, to get scutella and prevent precocious germination. Embryos of size 0.7–1.2 mm (slightly translucent immature embryos) are generally the most responsive, but there is genotypic variation (see Note 17 and Fig. 1). 2. Place 30 scutella (5 × 6) within central (approximately 2 cm diameter) target area in a 9 cm Petri dish containing induction medium (MS9%0.5DAg). Orientate them with the uncut scutellum up, i.e. the uncut side is bombarded. 3. Pre-culture the prepared donor material in the dark at 23 ± 1°C for 36–48 h prior to bombardment. The pre-culture allows to

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recover the tissues from the isolation procedure and to discard any contaminated explants. 3.1.3. Gold Suspension Preparation

1. Weigh 40 mg gold particles (0.6 μm) in a 1.5-mL Eppendorf tube, add 1 mL 100% ethanol, vortex, and sonicate in water bath for 90 s. Pulse-spin in a microfuge for 3 s and remove the supernatant. Repeat this ethanol wash once in 100% ethanol and once in 70% ethanol. 2. Add 1 mL sterile water, vortex, and sonicate for 90 s. Pulsespin in a microfuge for 3 s and discard the supernatant. Repeat this step once. 3. Re-suspend gold particles fully by vortexing in 1 mL sterile water. Aliquot 50 μL suspension into sterile 1.5-mL Eppendorf tubes. Do not forget to vortex between each pipetting to ensure an equal distribution of particles. Store the aliquots at −20°C for maximum 6 months.

3.1.4. Coating the Gold Particles with DNA for Bombardment

Each step of the procedure is carried out on ice in a sterile environment. 1. Allow a 50 μL aliquot of prepared gold (see Subheading 3.1.3) to thaw at room temperature. Vortex and then sonicate for 90 s (see Note 18). If the aliquots are going to be subdivided for smaller preparations (fewer shots), vortex in between taking aliquots is advisable. Volume(s) of solutions added later are scaled down accordingly. 2. Add 5 μg DNA (5 μL of 1 mg/mL in TE) or 5 μL sterile water (to replace DNA for bombarded controls) and vortex briefly to ensure good contact of DNA with the particles (see Note 19). 3. Place 44 μL 3 M CaCl2 and 20 μL 0.1 M spermidine first onto the side of the Eppendorf tube and mix together using the pipette tips. It helps to make coating as even as possible because DNA binds with them very rapidly. Mix the solution with the gold + DNA suspension by vortexing briefly. Pulsespin twice for 3–5 s in a microfuge to pellet the DNA-coated particles. Discard the supernatant. 4. Add 150 μL 100% ethanol to wash the particles. Re-suspend them as fully as possible by scraping the side of the tube with the pipette tip to remove clumps, and drawing up and expelling the suspension repeatedly. This is a crucial step since clumps cannot be removed later by vortexing. Pulse-spin twice for 3–5 s in a microfuge to pellet the DNA-coated particles and discard the supernatant. Repeat this step once. 5. Re-suspend the particles completely in 85 μL 100% ethanol and keep the tube(s) on ice. Use the DNA-coated gold suspension as soon as possible or keep on ice for no longer than 1 h.

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In this latter case, seal the Eppendorf lid(s) with Parafilm to reduce evaporation of the ethanol (see Note 20). 3.1.5. Particle Bombardment Using the PDS-1000/He Particle Gun (Bio-Rad)

When operating the gun, appropriate safety precautions should be taken as the delivery system involves the use of helium gas at high pressure to accelerate gold particles at high velocity. Include various control plates (non-bombarded controls (NBC) and bombarded controls (BC)) within each experiment to monitor regeneration and selection efficiencies (see Note 21). 1. Deliver the DNA-coated gold particles (see Subheading 3.1.4) into the target tissue according to the manufacturer’s instructions (Bio-Rad). Standard settings in the procedure are the gap (distance between rupture disc and macrocarrier, 2.5 cm), stopping plate aperture (distance between macrocarrier and stopping screen, 0.8 cm), target distance (between stopping screen and target plate, 5.5 cm). The vacuum is 27–28 in.Hg (91.4– 94.8 kPa), vacuum flow rate 5.0, vent flow rate 4.5 (54). 2. Sterilize the gun’s chamber and all the component parts by spraying with 70% (v/v) ethanol. Allow the ethanol to evaporate completely (~5 min). 3. Sterilize macrocarrier holders, macrocarriers, stopping screens, and rupture discs by dipping in 100% ethanol. Do not soak rupture discs in ethanol for more than 5 min or the laminate layers may become separated. Allow the alcohol to evaporate completely on a mesh rack or on Petri dishes in a flow hood. Place three or four macrocarrier holders into a sterile 9-cm Petri dish. Put one dry macrocarrier into each holder and push it down using the red seating tool. The edge of the macrocarrier should be securely inserted under the lip of the macrocarrier holder. 4. Briefly vortex the coated gold particles (see Subheading 3.1.4), take 5 μL and spread evenly over the central 1 cm of the macrocarrier membrane in the holder. Load only three or four macrocarriers at one time and cover the Petri dish with its lid immediately. Allow gold suspension to dry naturally outside of the flow hood but on a non-vibrating surface in order to avoid particle agglomeration (see Note 22). 5. Load a rupture disc (either 650 or 900 psi; 4.484 or 6.209 MPa) into the rupture disc retaining cap and screw into place on the gas acceleration tube. Tighten it firmly using the mini torque wrench (see Note 23). 6. Place a stopping screen into the fixed nest. Invert the macrocarrier holder containing macrocarrier with DNA-coated gold particles and put over the stopping screen in the nest (dried particles should be facing down toward the stopping screen). Replace the macrocarrier cover lid on the assembly and turn

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clockwise until snug, but do not over-tighten. Put the fixed nest assembly onto the second shelf from the top to give a gap of 2.5 cm. 7. Place the Petri dish carrying the tissue samples on the appropriate shelf to give the required distance (5.5 cm, fourth shelf from the top) from the stopping screen. 8. Draw a vacuum of 27–28 in.Hg (91.4–94.8 kPa) and fire the gun. The helium pressure builds up, breaks the rupture disc, moves the macrocarrier onto the stopping plate, and thus the DNA-coated particles are released and dispersed. Monitor the actual pressure at which the rupture disc bursts to ensure successful shot (may affect transformation efficiency). 9. Release the vacuum, remove the tissue samples (put the lid to the Petri dish first), and disassemble the component parts. Collect or discard the ruptured disc and macrocarrier (see Note 24). 10. Place the macrocarrier holder and stopping screen in 100% ethanol to re-sterilize if they are to be reused for further shots. 11. Remember to bombard two to three Petri dishes (BC) with gold (no DNA) to monitor the effect of bombardment and the selection efficiency later (see Note 25). 3.1.6. Induction of Embryogenic Calli from Immature Scutella Following Bombardment

1. After bombardment, spread the scutella evenly across the induction medium (CI/Biol, see Subheading 2.1.4) in 9-cm Petri dishes. To prevent competition for nutrients, divide each replicate between three plates (one is the original) (10 scutella per plate). 2. Seal the plates with plastic film (Parafilm or PE film) and incubate for 3 weeks at 23 ± 1°C in the dark for induction of embryogenic calli. Check regularly for contamination. After 2–3 days, transient assays e.g. histochemical GUS assay, can be carried out (see Subheading 3.3.2). Using stereomicroscope, observe calli randomly for visible nodular outgrowth (called embryogenic calli).

3.1.7. Regeneration and Selection of Transgenic Plants

1. Stage 1. Regeneration, without selection: after 3 weeks on callus induction medium, transfer calli bearing somatic embryos to regeneration medium (RZD + 1/2Cu, see Subheading 2.1.4) in 9 cm Petri dishes. Discard any hydrated and necrotic ones. Transfer whole calli without division (7–8 calli per plate) and incubate at 23 ± 1°C in the light for 3 weeks (see Notes 26 and 27). By the end of the third week, shoots and green structures should appear. 2. Stage 2. Regeneration with selection: after 3 (or maximum 6) weeks, transfer calli bearing shoots without division onto RZ + selection media in 9 cm Petri dishes with RZPPT2

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medium (see Note 11). Incubate at 23 ± 1°C in the light for 3 weeks. Culture 7–8 calli per Petri dish of controls (NBC, BC) on media with and without (RZ, see Subheading 2.1.4) selection agent too. Apply selection from now on, until all control plantlets have been killed (see Note 11). 3. Stage 3. Regeneration with selection: after a further 3 weeks, and every subsequent 3 weeks, transfer surviving (healthy and responsive) calli with shoots to regeneration medium + selection agent but without hormones (RPPT3-4, see Note 11) in 9-cm Petri dishes (5–6 calli per plate). Discard any unresponsive calli. Transfer calli with shoots from control plates onto R0 and RPPT3-4 in Petri dishes. Incubate them in the light at 23 ± 1°C or at 25–26°C to shorten tissue culture period, provided another plant room is available. 4. Root regeneration with selection: separate 3–4 cm long plantlets with small or definite roots from the callus and transfer to RPPT4 media but in GA-7 Magenta vessels. Place only 3–4 plantlets per Magenta and incubate in the light (see step 3 in Subheading 3.1.7). 5. Transfer plantlets (>10 cm in length) with established root system to Jiffy pots (see Note 28) or vernalize winter wheat varieties on R0 media in Magenta vessels at 4°C for 6 weeks. Remove plantlets carefully from the Agargel (solidified medium). If they are to be planted into Jiffy pots, rinse the roots with tap water before potting. Grow them in a GM containment chamber, initially within a propagator (or in plastic bags) to provide high humidity for 12–14 days to acclimatize from tissue culture (see Note 29). 6. Pot the 3 and 4 leaf stage plants to 13 cm diameter pots and grow them to maturity in separate growth chambers for GM but under conditions similar to those used for donor plants. Plants should reach maturity in 3 months (it takes 4 and a half months for winter wheat varieties). 3.2. Method for AgrobacteriumMediated Transformation

Wheat (T. aestivum L.) plants (cv. Cadenza, Fielder, Florida, and different elite varieties) and tetraploid durum wheat (T. turgidum L. var. durum) are grown under controlled conditions in phytotron chamber as it is described in Subheading 2.1.1.

3.2.1. Growth of Donor Plants 3.2.2. Preparation of Agrobacterium Cells for Inoculation

1. Initiate Agrobacterium liquid cultures by adding ~200 μL of a standard glycerol inoculum to 10 mL MG/L (see item 2 in Subheading 2.2.2) plus antibiotics (see Note 30). Prepare as many 10 mL cultures as plates (Petri dishes with 50 scutella in each) to be treated.

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2. Incubate at 28–29°C, shaking (250 rpm) for 16–20 h (usually overnight) to reach an OD > 1 (optical density). Measure absorbance at 600 nm. 3. Pellet the Agrobacterium culture at 4,500 × g for 10 min and re-suspend the bacteria in 4 mL single-strength inoculation medium (see item 2 in Subheading 2.2.4) supplemented with 200 μM acetosyringone (see Note 31) for each culture (originally 10 mL). 4. Put the suspended cultures back to the shaker until required, but they should be used within 3 h. 3.2.3. Collection and Sterilization of Wheat Caryopses 3.2.4. Isolation of Immature Scutella and Inoculation with A. tumefaciens

Collect spikes from phytotron chambers-grown plants 12–14 days post anthesis (DPA) and sterilize as it is described in steps 1–4 in Subheading 3.1.1. 1. Isolate immature scutella microscopically in sterile environment with sharp scalpel while removing the embryo axis (see step 1 in Subheading 3.1.2). 2. Place 50 scutella with the axis side (now removed) down onto semi-solid inoculation medium (see Subheading 2.2.4) in 5.5 or 9 cm Petri dish, within the central area of ~3 or 6 cm diameter. Before isolating scutella for the next plate, it is important to inoculate each plate of 50 scutella with A. tumefaciens, as described below (see steps 3–5). 3. Take the re-suspended Agrobacterium out of the shaker, add 60 μL 1% Silwet, mix, and pour the whole 4 mL over a batch of 50 plated scutella. 4. Incubate for 1–2 h in the dark at room temperature while preparing more scutella for inoculation as described in step 1 in Subheading 3.1.2 and step 2 in Subheading 3.2.4. 5. Pipette off the Agrobacterium cells. Transfer scutella without blotting, keeping the ex-axis side down, onto fresh inoculation medium in Petri dishes. Spread 12–13 calli per plate. Allow to co-cultivate in the dark at 23 ± 1°C for 3 days. 6. Within each experiment, prepare scutella (30/dish) for negative control plates to monitor regeneration and selection efficiencies.

3.2.5. Induction of Embryogenic Calli, Regeneration and Selection of Transgenic Plant

Use antibiotic timentin (150 mg/L) to inhibit the growth of A. tumefaciens cells during the embryogenic callus phase, and in all the subsequent media including regeneration and two rounds of selection, each for 3 weeks. 1. Callus induction: after 3 days of co-cultivation in the dark, transfer all scutella (12–13 calli per plate) to semi-solid induction medium (see Subheading 2.2.4) and continue to incubate in the dark at 23 ± 1°C for 18 days.

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2. Stage 1. Regeneration, without selection: after 18 days, transfer embryogenic calli to regeneration medium (R/inDTZ, see Subheading 2.2.4). Discard any hydrated and necrotic ones. Incubate 7–8 calli only per plate at 23 ± 1°C, but in the light (see step 1 in Subheading 3.1.7). Keep embryogenic calli derived from the same immature embryo intact without breaking up. 3. Stage 2–3. Regeneration with selection: after 3 weeks, transfer embryogenic calli and plantlets from Stage 1 to selection medium, called R/inT-PPT (see Note 11). Put only 5–6 calli with shoots onto one plate. Discard any unresponsive one (see Note 32). Culture 7–8 calli per Petri dish of negative controls on media with and without (R/inT, see Subheading 2.2.4) selection agent too. Apply selection from now on (see Note 33), until all control plantlets have been killed (see Note 11). 4. Continue transferring calli and plantlets to fresh R/inT-PPT media in Petri dishes for shoot regeneration, and in Magenta vessels for root regeneration and strengthening, respectively. Subculture every 3 weeks until PPT tolerant plantlets are ready to be potted to Jiffy pots, then to soil (see Note 34). (See also steps 5 and 6 in Subheading 3.1.7 at the biolistic transformation method). 3.3. Analysis of the Regenerated Transgenic Wheat Plants

Transgenic plants can be analyzed in a number of ways, but below we show only how the reporter/marker gene expression can be assessed. The histochemical GUS test (see Subheadings 3.3.2 and 3.3.3) was used to monitor the uidA gene expression. For bar gene expression the herbicide leaf paint assay, the ammonium test and/ or the PAT assay (spray test) were used (see Subheading 3.3.4). The presence of recombinant DNA can be determined using PCR method (see Subheading 3.3.1); however, it should be noted that PCR does not confirm stable transgene integration into the plant genome. Additional analyses can be performed to identify the site of genomic integration, estimate copy number, confirm inheritance/segregation using, for example, southern analysis, fluorescent in situ hybridization (FISH) and/or qPCR, but these methods are not described here.

3.3.1. Screening the Primary Regenerated Plantlets (T0 Transgenic Plants) by PCR

When plants are large enough (3 and 4 leaf stage) collect 25–40 mg leaf material, and extract genomic DNA using any commercially available extraction kit (see Note 14). Both the bar and the uidA genes can be detected by PCR using the primers and conditions detailed below.

Detecting the bar Gene

Forward primer: 5¢ GTCTGCACCATCGTCAACC 3¢ Reverse primer: 5¢ GAAGTCCAGCTGCCAGAAAC 3¢ Product size: 444 bp.

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Carry out the PCR analysis in 10 μL reaction mixture containing one volume Taq PCR buffer, 0.1 mM dNTPs, 0.5 μM of each primer, 1.25 U Go Taq polymerase (Promega), and ~80 ng genomic DNA. After initial denaturation (95°C for 5 min), apply the following cycling conditions: 36 cycles at 95°C for 30 s (denaturation), 60°C for 60 s (annealing), 72°C for 30 s (elongation), followed by a final extension at 72°C for 5 min. Analyze PCR products (444 bp) by electrophoresis in 1.0% agarose gel. Detecting the uidA Gene

Forward primer: 5¢ TACGTATCACCGTTTGTGTGAAC 3¢ Reverse primer: 5¢ CCGCTTTGGACATACCATCCGTA 3¢ Product size: 1,042 bp. Carry out the PCR analysis as it is described for detecting bar gene; however, use 1 min as elongation time.

3.3.2. Histochemical GUS Assay for Transient Expression

The uidA gene encodes the β-glucuronidase (GUS) enzyme whose activity can be measured using a histochemical (GUS) assay (see Note 35). 1. Two to three days after bombardment (time depending on the construct i.e. strength of the promoter) remove two scutella from four dishes each of control and treated with DNA. Place scutella separately into the wells of a microtitre plates with X-Glca (or X-Gluc) solution (50–80 μL in each well). 2. Seal the plate with Parafilm and incubate overnight in a thermostat at 37°C. 3. Place the samples (scutella) under a stereomicroscope to visualize and count the blue, GUS-expressing spots.

3.3.3. Stable Expression of uidA Gene (GUS Activity Assay) Leaf Segment Test

At the end of the first round of selection in Petri dishes, some of the T0 transgenic plants may be identified by GUS assay. 1. Place ½ cm long leaf fragments into the wells of a microtitre plate with 100 μL X-Glca (or X-Gluc) solution in each well (see Note 36). 2. Seal the wells and incubate the samples overnight in a thermostat at 37°C. If necessary, incubate at 25°C for a further 24 h for the colour to fully develop. 3. After incubation, remove the chlorophyll in leaf fragments by replacing X-Glca (or X-Gluc) with 70% ethanol under light until the green colour faded and blue diXH-indigo product is clearly visible. 4. The plantlets tested positive and with good strong roots may be transferred to Jiffy pots, then to soil. Winter wheat varieties should be put into the vernalization room first. Plantlets with shoots only or weak root system should be transferred to R medium without PPT selection agent in Magenta vessels for root strengthening.

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Testing GUS Activity in Dry Seed Segments

The stable expression of uidA gene by the method described above can be performed on a thin cross section of dry seeds, as well. 1. Cut 1–1.5 mm cross sections of the dry seeds opposite to the embryo side (see Note 37) and put them into the wells of a marked microplate (one in each well). 2. Incubate the tissues fully immersed in X-Glca (or X-Gluc) solution (150–200 μL) in conditions as for leaf segment test. 3. Germinate the embryo-containing part of the seed if the correlating segment tested positive (see Note 37).

3.3.4. Stable Expression of the bar Gene: PAT Assay for the Selection of Herbicide Resistant

Resistance to herbicides can be evaluated in established primary transgenic plants (T0 generation) and their progeny (T1 and subsequent generations).

Transgenic Lines Leaf Painting Bioassay

This approach for qualitative expression of the bar gene is simple and inexpensive and can be carried out on plants in situ. 1. Prepare dilutions of glufosinate ammonium-based herbicide using 0.1% Tween-20 to give final concentrations of the PPT solution of 0.2 g/L and 2 g/L (see Note 6). 2. Select healthy wheat plants at the tillering phase of growth. For each plant to be tested, select 3 approximately equal sized, healthy leaves, except for the flag leaf. Water the plants before herbicide application. 3. Label the three chosen leaves on the stem right below the leaf to be treated: “Tween only” for controls, 0.2 g/L PPT, and 2 g/L PPT. 4. Mark each leaf with a ballpoint pen halfway along its length and paint the upper surface of the distal half of the leaf with the appropriate solution using a cotton bud (see Note 38). Paint all the control leaves first (Tween only), followed by the lower concentration (0.2 g/L), then the higher concentration (2 g/L) of herbicide to minimize carry-over of the herbicide to other leaves. 5. Assess the herbicide resistance of each plant 7 days after application by scoring each treated leaf according to the percentage desiccation/browning over the painted area and the percentage of the proximal region of the leaf that has been affected by the spread of the herbicide (see Note 39).

Qualitative Ammonium Test

1. Place 4 × 8 mm leaf pieces in 25-multiwell plates containing 1 mL incubation medium (see Subheading 2.3.3) per well, leaving 1 or 2 wells without tissue as negative controls (see Note 40).

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2. Incubate at 24°C under a photosynthetic photon flux density of 250 μmol/m2 s for 5 h (see Note 41). 3. Take out 200 μL of the incubation medium of each sample and add to 1 mL of Reagent 1 (see Note 42). 4. Add 1 mL of Reagent 2 to the mix and vortex it. 5. Incubate at 37°C for 15 min, followed by 15 min incubation at room temperature. 6. Evaluate the result according to the colour developed in the solutions (see Note 43). Quantitative Ammonium Test

1. Place 4 × 8 mm leaf pieces in 25-multiwell plates. Proceed as for the qualitative assay. 2. Prepare a standard curve with increasing concentrations of ammonium chloride by adding 200 μL of standard solutions of ammonium (from 0 to 10 mg/L) to the mixture of 1 mL Reagent 1 plus 1 mL Reagent 2 (see Note 42), then incubate as in step 5 for the qualitative assay. 3. Measure the absorbance of each solution at 655 nm. 4. Determine the concentration of ammonium ion in each sample using the standard curve.

PAT Assay (Spraying Transgenic Plants at Their Five- or Six-Leaf Stage)

Transgenic plants resistant to the herbicide can also be identified by a spraying test (see Note 44). 1. Spray 12 (or 16) plants for each line twice (2 days in between) at their five- or six-leaf stage with 1 g/L glufosinate ammonium-based solution (see Note 6). 2. Assess (i.e. count the number of survived plants) the herbicide resistance of the plants 2 weeks after the treatment. Let healthy strong plants to grow and to set seeds.

4. Notes 1. It is important to avoid any stress to the donor plants. Apply routine pesticide and fertilizing treatments in every 15 days/ fortnightly, but it should be avoided from pollination to harvest time. 2. Commercially available 10% (v/v) aqueous Domestos solution can be applied without surfactant as it contains detergent as well. 3. Weigh solutes in weighing boats and then transfer each component separately to a glass beaker containing 600 mL ultrapure water. Allow solutes to dissolve completely one after the

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other on magnetic stirrer. Note that CaCl2 dissolves slowly. Pour solution into a graduated cylinder and then add ultrapure water to a volume of 1 L. If 100–400 mL of solutions are going to be prepared, scale-down the amounts of each component accordingly. 4. Filter sterilization is carried out using Steritop 0.22-μm filters, Millipore. For small volumes of solutions (5–50 mL), use disc syringe filter. For larger volumes (0.2–2 L) use for example MediaKap® filters which are operated by gravity or under pressure, using a peristaltic pump or pressure vessel. 5. Silver nitrate (used to promote embryogenesis) is photosensitive, so stock solution and all media plates containing it must be stored in the dark. 6. For selection media preparation it is recommended to use synthetic l-phosphinothricin (PPT) selection agent at the concentration of 2–4 mg/L, which provides successful selection. For analysis of stable expression of the bar gene (PAT assay, see Subheading 3.3.4), glufosinate ammonium-based solutions are recommended. Glufosinate ammonium is a synthetically produced PPT bound to ammonium and is the active component in herbicides such as Basta™, Bialaphos, or FINALE. Be aware of that the various commercially available formulations contain different concentrations of the active ingredient. 7. When preparing double-strength tissue culture media add the ferrous sulphate chelate stock solution first (or ethylenediaminetetraacetate disodium salt, see item 1 in Subheading 2.1.3) to the distilled water to keep other components dissolved. 8. Filter-sterilize only 400 mL double-strength tissue culture medium into a sterile 1 L bottle to give space for the addition of melted double-strength Agargel (or Phytagel) when preparing the working medium later. 9. Allow to cool the melted gelling agent to 50°C in a water bath. Warm up the double-strength tissue culture medium in the water bath too, before mixing it with the double-strength melted gellig agent. 10. At this high concentration (9%) of sucrose in the medium, the walls of the cells shrink due to the loss of water through osmosis during pre-culture, which may allow them to better withstand bombardment. But 3% sucrose is often suitable e.g. for T. turgidum ssp. durum scutella (42). 11. The concentration of PPT selection agent (2–4 mg/L) applied in the medium depends on the wheat variety to be transformed. Trial experiments are needed to assess the level of selection agent that is studied to fully inhibit the growth of non-transformed explants. Above all, it is recommended to use the selection agent at the lowest concentration (2 mg/L) in

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the first round of selection, then increase it to the maximum of 4 mg/L (usually 3–4 mg/L). 12. The transformation cassette, carried in the plasmid pAHC25, contains the selectable marker gene bar and the uidA reporter gene, both driven by the constitutive promoter ubiquitin1, also containing the ubiquitin1 intron from maize. 13. For Agrobacterium-mediated transformation the AGL1 A. tumefaciens strain was used (46). This super-virulent strain contains the plasmids pAL154/pAL156 based on the plasmid pSoup/pGreen (47). The single T-DNA in binary vector pAL156 incorporates the bar gene and a modified uidA gene with an intron within the open reading frame to prevent its expression in Agrobacterium itself; both genes are driven by the maize ubiquitin1 promoter also carrying the ubiquitin1 intron (45). The bar gene is located next to the left border, and uidA is adjacent to the right border. The plasmid pAL154 helps the replication functions for pAL156 in trans and contains the 15 kb Komari fragment (48, 49) supplying extra vir genes. 14. To purify DNA for PCR, kits such as AquaGenomic, ExtractN-Amp, QIAGEN, or Wizard® Genomic DNA Purification Kit may also be used. If the DNA is used for southern blot analysis as well, the CTAB method (55) is recommended (not provided in this Chapter). 15. Store sodium nitroprusside containing solutions in the dark, as it slowly breaks down to release cyanide ions, especially upon exposure to UV light. 16. Sodium dichloroisocyanurate is a stabilized chlorine donor containing cyanuric acid and used as a disinfectant. Store the solution for maximum 2 months to keep it effective. 17. Smaller and larger embryos than 0.7–1.2 mm may respond but with much lower efficiencies. Better to keep scutella from this size of embryos on separate Petri dishes. 18. After efficient sonication, gold particles should be re-suspended in the liquid rather than be present as a pellet in the base of the tube, but either shorter than 60 s or longer than 2 min sonication could promote agglomeration of gold particles. 19. For co-bombardment, use equimolar amounts of DNA not more than a total of 5 μg for the two cassettes, which may reduce clumping of gold particles. 20. Although 85 μl of gold suspension should be sufficient for 16–17 shots (5 μL/shot), it is generally enough for only 10–12 shots because of evaporation during the work. 21. Non-bombarded controls (NBC) monitor the development/ regeneration of donor tissue. Bombarded controls (BC) with

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gold only (no DNA) without selection are used to monitor the tissue culture response following the bombardment. Bombarded controls with gold only (no DNA) with selection monitor the effects of the selection on regeneration. 22. Let the ethanol evaporate for not longer than 10 min; otherwise, the coated gold particles would adhere to the macrocarrier too strongly to release them at shooting. Check macrocarriers microscopically prior to bombardment for the uniformity of particles (spread of particles) and discard any that may have clumps of gold. 23. Remember to set the helium pressure on the cylinder to approximately 200 psi (1.38 MPa) more than the intended rupture pressure, which is genotype dependent and should be studied empirically. 24. Check the macrocarriers under a stereomicroscope after the shot, to visualize the mesh pattern left by the stopping screen and check how much gold has been released/retained. 25. Do not bombard 2 Petri dishes (NBC) out of 10 or 15 dishes to monitor regeneration efficiency of target tissue. 26. Light source should be white cool fluorescent tubes (20 μmol/m2 s PAR for a 16-h photoperiod). Covering the plates with 10–15 layers of PE film (thickness of 25 μm) during the first week may reduce the light shock to the tissues and may increase the number of leafy structures. 27. If the regeneration response is poor, i.e. if no shoots appear, repeat one round of regeneration (up to 3 weeks) on fresh medium without selection agent (RZD + 1/2Cu). 28. It takes usually at least 3 months from bombardment to get plantlets (>10 cm in length) with an established root system. 29. Small plantlets have little or no waxy cuticle and are particularly prone to desiccation. 30. The antibiotics used depend on the selectable markers in the Agrobacterium strain and binary vectors. 31. Add 16 μL of the stock solution (50 mM) (see item 6 in Subheading 2.2.3). Use 400 μM acetosyringone for tetraploid durum wheat (T. turgidum L. var. durum; cv. Ofanto) (44). 32. At this point, the regenerating callus pieces may be divided into defined shoots/roots (or accidentally break into pieces) when transferred, but it is important to keep these together, or mark them clearly, as there is a possibility that these may be clones. 33. Some of the transgenic plants may be identified by GUS assay on leaf fragments at the end of the first round of selection (see Subheading 3.3.3).

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34. If they have good strong roots, they may be transferred to soil or put into the vernalization room immediately. Otherwise, transfer them to R/inT medium without PPT for root strengthening. 35. The GUS enzyme (expressing in transgenic plant tissues) hydrolyzes the X-Gluc (or X-Glca) substrate to give an insoluble and highly coloured indigo dye. This blue precipitate can be visualized at the site of enzyme activity or easily detectable by quantitative (fluorometric or spectrophotometric) analysis. 36. With this assay, the stable expression of the uidA gene can be monitored not only in embryogenic calli and leaf fragments but in roots, anthers, pollen, and ovaries as well. 37. Keep the embryo parts of the tested seeds separately in marked microplates. If the segments were tested positive, germinate the corresponding embryo-containing parts of the seeds. Transfer plantlets into soil then grow in environmentally controlled growing chamber to set seeds. 38. The application should be firm to ensure coating and some penetration of the solution into the leaf tissue. 39. The application of the herbicides based on glufosinateammonium causes desiccation and browning in control plants, whereas plants carrying the bar gene and synthesizing the appropriate enzyme are resistant and remain green. 40. Choose young, green leaves for this assay. Set incubations up in a laminar flow hood to avoid contamination. Ensure that leaf pieces are fully immersed in the incubation medium; this can be achieved by briefly shaking the plates by hand. 41. Tissue culture room is adequate for this purpose. 42. The assay is performed in either microplate or cuvette, but having large number of samples to test, microplate is recommended. 43. The incubation medium with plant samples not expressing the bar gene and the negative controls will develop an emerald green to dark-blue colour due to the presence of ammonium ions. The medium of explants from transgenic plants expressing the enzyme coded by the bar gene will develop a light green or yellow colour that occurs in the absence of ammonium ions. 44. When the transformation is done by co-bombardment of the selectable marker and gene of interest on separate plasmids, selection pressure will kill plants that have taken up only the gene of interest, as they are not resistant to herbicide. In the experience of the authors, only about 10–20% of independent transgenic plants possess only one of the plasmids in a cobombardment experiment.

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Acknowledgements László Tamás is in receipt of grants from the Hungarian Scientific Research Fund (OTKA T 46703 and 67844) and of the Bilateral Intergovernmental Science and Technology Cooperation (KR1/2007). Rothamsted Research receives grant-aided support from the Biotechnology and Biological Sciences Research Council of the United Kingdom. References 1. Vasil V et al (1992) Herbicide resistant fertile transgenic wheat plants obtained by microprojectile bombardment of regenerable embryogenic callus. Bio/Technology 10: 667–674 2. Vasil IK (2007) Molecular genetic improvement of cereals: transgenic wheat (Triticum aestivum L.). Plant Cell Rep 26:1133–1154 3. Jones HD (2005) Wheat transformation: current technology and applications to grain development and composition. J Cereal Sci 41: 137–147 4. Jones HD et al (2005) Review of methodologies and a protocol for the Agrobacteriummediated transformation of wheat. Plant Methods 1:5 5. Cheng M et al (2004) Factors influencing Agrobacterium-mediated transformation of monocotyledonous species. In Vitro Cell Dev Biol Plant 40:31–45 6. Shewry PR, Jones HD (2005) Transgenic wheat: where do we stand after the first 12 years? Ann Appl Biol 147:1–14 7. Patnaik D, Khurana P (2001) Wheat biotechnology: a minireview. Electron J Biotechnol 4:2 8. Barcelo P et al (2001) Transformation and gene expression. In: Shewry PR, Lazzeri PA, Edwards KJ (eds) Advances in botanical research incorporating advances in plant pathology. Academic, San Diego 9. Blechl AE, Jones HD (2009) Transgenic applications in wheat improvement. In: Carver BF (ed) Wheat; sciences and trade. Wiley, Iowa 10. Altpeter F et al (2005) Particle bombardment and the genetic enhancement of crops: myths and realities. Mol Breed 15:305–327 11. Hensel G et al (2009) Agrobacterium-mediated gene transfer to cereal crop plants: current protocols for barley, wheat, triticale, and maize. Int J Plant Genom 2009:9, Article ID 835608

12. Pellegrineschi A et al (2004) Stress-induced expression in wheat of the Arabidopsis thaliana DREB1A gene delays water stress symptoms under greenhouse conditions. Genome 47:493–500 13. Fahim M et al (2010) Hairpin RNA derived from viral NIa gene confers immunity to wheat streak mosaic virus infection in transgenic wheat plants. Plant Biotechnol J 8:821–834 14. Gao SQ et al (2009) A cotton (Gossypium hirsutum) DRE-binding transcription factor gene, GhDREB, confers enhanced tolerance to drought, high salt, and freezing stresses in transgenic wheat. Plant Cell Rep 28:301–311 15. Xu ZS et al (2007) Isolation and molecular characterization of the Triticum aestivum L. ethylene-responsive factor 1 (TaERF1) that increases multiple stress tolerance. Plant Mol Biol 65:719–732 16. Yu Y, Wei ZM (2008) Increased oriental armyworm and aphid resistance in transgenic wheat stably expressing Bacillus thuringiensis (Bt) endotoxin and Pinellia ternate agglutinin (PTA). Plant Cell Tissue Organ Cult 94: 33–44 17. Altpeter F et al (1996) Integration and expression of the high-molecular-weight glutenin subunit 1Ax1 gene into wheat. Nat Biotechnol 14:1155–1159 18. Blechl AE, Anderson OD (1996) Expression of a novel high-molecular-weight glutenin subunit gene in transgenic wheat. Nat Biotechnol 14:875–879 19. Barro F et al (1997) Transformation of wheat with high molecular weight subunit genes results in improved functional properties. Nat Biotechnol 15:1295–1299 20. Alvarez ML et al (2000) Silencing of HMW glutenins in transgenic wheat expressing extra HMW subunits. Theor Appl Genet 100: 319–327

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21. Field JM et al (2008) Introgression of transgenes into a commercial cultivar confirms differential effects of HMW subunits 1Ax1 and 1Dx5 on gluten properties. J Cereal Sci 48:457–463 22. Zhang XD et al (2003) Transgene inheritance and quality improvement by expressing novel HMW glutenin subunit (HMW-GS) genes in winter wheat. Chin Sci Bull 48:771–776 23. Bregitzer P et al (2006) Changes in high molecular weight glutenin subunit composition can be genetically engineered without affecting wheat agronomic performance. Crop Sci 46:1553–1563 24. Anderson OD, Blechl AE (2000) Transgenic wheat—challenges and opportunities. In: O’Brian L, Henry R (eds) Transgenic cereals. AACC, St Paul 25. Shewry PR, Jones HD (2007) Genetic improvement of wheat quality. In: Pomeranz Y (ed) Wheat: chemistry and technology (AACC Monograph Series). American Association of Cereal Chemists, Washington 26. Vasil IK et al (2001) Evaluation of baking properties and gluten protein composition of field grown transgenic wheat lines expressing high molecular weight glutenin gene 1Ax1. J Plant Physiol 158:521–528 27. Rakszegi M et al (2005) Technological quality of transgenic wheat expressing an increased amount of a HMW glutenin subunit. J Cereal Sci 42:15–23 28. Rakszegi M et al (2008) Technological quality of field grown transgenic lines of commercial wheat cultivars expressing the 1Ax1 HMW glutenin subunit gene. J Cereal Sci 47:310–321 29. Shewry PR et al (2006) Comparative field performance over 3 years and two sites of transgenic wheat lines expressing HMW subunit transgenes. Theor Appl Genet 113:128–136 30. Masci S et al (2003) Production and characterization of a transgenic bread wheat line overexpressing a low-molecular-weight glutenin subunit gene. Mol Breed 12:209–222 31. Tosi P et al (2004) Expression of epitopetagged LMW glutenin subunits in the starchy endosperm of transgenic wheat and their incorporation into glutenin polymers. Theor Appl Genet 108:468–476 32. Tosi P et al (2005) Modification of the low molecular weight (LMW) glutenin composition of transgenic durum wheat: effects on glutenin polymer size and gluten functionality. Mol Breed 16:113–126 33. Shewry PR (2007) Improving the protein content and composition of cereal grain. J Cereal Sci 46:239–250

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34. Zhu C et al (2007) Transgenic strategies for the nutritional enhancement of plants. Trends Plant Sci 12:548–555 35. Regina A et al (2006) High-amylose wheat generated by RNA interference improves indices of large-bowel health in rats. Proc Natl Acad Sci USA 103:3546–3551 36. Tamas C et al (2009) Transgenic approach to improve wheat (Triticum aestivum L.) nutritional quality. Plant Cell Rep 28:1085–1094 37. Lamacchia C et al (2001) Endosperm-specific activity of a storage protein gene promoter in transgenic wheat seed. J Exp Bot 52:243–250 38. Wiley PR et al (2007) Promoter analysis and immunolocalisation show that puroindoline genes are exclusively expressed in starchy endosperm cells of wheat grain. Plant Mol Biol 64(1–2):125–136 39. Van Herpen T et al (2008) Detailed analysis of the expression of an alpha-gliadin promoter and the deposition of alpha-gliadin protein during wheat grain development. Ann Bot 102:331–342 40. Oszvald M et al (2008) Development and charatcterization of a chimaeric tissue-specific promoter in wheat and rice endosperm. In Vitro Cell Dev Biol Plant 44:1–7 41. Stoger E et al (2000) Cereal crops as viable production and storage systems for pharmaceutical scFv antibodies. Plant Mol Biol 42:583–590 42. Sparks CA, Jones HD (2004) Transformation of wheat by biolistics. In: Curtis IP (ed) Transgenic crops of the world—essential protocols. Kluwer Academic, Dordrecht 43. Tamas C et al (2004) Effect of combined changes in culture medium and incubation conditions on the regeneration from immature embryos of elite varieties of winter wheat. Plant Cell Tissue Organ Cult 79:39–44 44. Wu HX et al (2008) Efficient and rapid Agrobacterium-mediated genetic transformation of durum wheat (Triticum turgidum L-var. durum) using additional virulence genes. Transgenic Res 17:425–436 45. Christensen AH, Quail PH (1996) Ubiquitin promoter-based vectors for high-level expression of selectable and/or screenable marker genes in monocotyledonous plants. Transgenic Res 5:213–218 46. Lazo GR et al (1991) A DNA transformationcompetent Arabidopsis genomic library in Agrobacterium. Bio/Technology 9:963–967 47. Hellens RP et al (2000) pGreen: a versatile and flexible binary Ti vector for Agrobacteriummediated plant transformation. Plant Mol Biol 42:819–832

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48. Komari T (1990) Transformation of culturedcells of Chenopodium quinoa by binary vectors that carry a fragment of DNA from the virulence region of pTiBo542. Plant Cell Rep 9:303–306 49. Komari T et al (1996) Vectors carrying two separate T-DNAs for co-transformation of higher plants mediated by Agrobacterium tumefaciens and segregation of transformants free from selection markers. Plant J 10: 165–174 50. Garfinkel DJ, Nester EW (1980) Agrobacterium tumefaciens mutants affected in crown gall tumorigenesis and octopine catabolism. J Bacteriol 144:732–743 51. RascoGaunt S, Barcelo P (1999) Immature inflorescence culture of cereals: a highly responsive system for regeneration and transformation. In: Hall R (ed) Methods in molecular

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biology—plant cell culture protocols. Humana, Totowa He GY, Lazzeri PA (2001) Improvement of somatic embryogenesis and plant regeneration from durum wheat (Triticum turgidum var. durum Desf.) scutellum and inflorescence cultures. Euphytica 119:369–376 Barcelo P et al (1994) Transgenic cereal (Tritordeum) plants obtained at high-efficiency by microprojectile bombardment of inflorescence tissue. Plant J 5:583–592 Rasco-Gaunt S et al (1999) Analysis of particle bombardment parameters to optimise DNA delivery into wheat tissues. Plant Cell Rep 19:118–127 Stacey J, Isaac P (1994) Isolation of DNA from plants. In: Isaac P (ed) Methods in molecular biology—protocols for nucleic acid analysis by nonradioactive probes. Humana, Totowa

Chapter 28 Improved Genetic Transformation of Cork Oak (Quercus suber L.) Rubén Álvarez-Fernández and Ricardo-Javier Ordás Abstract An Agrobacterium-mediated transformation system for selected mature Quercus suber L. trees has been established. Leaf-derived somatic embryos in an early stage of development are inoculated with an AGL1 strain harboring a kanamycin-selectable plasmid carrying the gene of interest. The transformed embryos are induced to germinate and the plantlets transferred to soil. This protocol, from adult cork oak to transformed plantlet, can be completed in about one and a half years. Transformation efficiencies (i.e., percentage of inoculated explants that yield independent transgenic embryogenic lines) vary depending on the cork oak genotype, reaching up to 43%. Key words: AGL1, Agrobacterium tumefaciens, Cork oak, Fagaceae, Herbicide resistance, Kanamycin resistance, Quercus suber, Somatic embryogenesis, Tree genetic transformation

1. Introduction Biotechnology has become a powerful tool for the introduction of foreign genes into long-lived perennials and for fundamental studies of gene expression (1–3). It can help to minimize difficulties associated with traditional breeding and reduce the time necessary to introduce traits, a very time-consuming process particularly in woody species. Moreover, this technology allows for the introduction of these traits without compromising the genetic background of the elite clone in the way classical breeding does, i.e., in one generation and avoiding the likely need for backcrosses. Biotechnological approaches have been successfully applied in the family Fagaceae, which includes financially important forest species that play a role in soil and environment conservation, CO2 assimilation, wood production and as energy resources. Genetic transformation protocols have been developed for the species this Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_28, © Springer Science+Business Media, LLC 2012

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chapter is devoted to, Quercus suber L. (4–6), and also for a few other Fagaceae: Castanea dentata (7–11), Castanea sativa (12– 16), Nothofagus alpina (17), and Quercus robur (18–20). Cork oaks (Q. suber L.) grow in the Mediterranean area (see a review on cork oak woodlands in (21)). These trees are among the most important ones in the dehesa (22), a managed ecosystem that also produces acorns—used to feed pigs—honey and, very importantly, cork. Many efforts have been done in cork oak breeding, but classical approaches in this species are constrained by its reproductive characteristics: a long juvenile period of up to 30 years, self-incompatibility and a high degree of heterozygosis, among others. This explains that, like other trees, it has undergone little domestication. However, in the past few years biotechnology has made available a very useful tool: somatic embryogenesis. A prerequisite for the production of transgenic plants is the availability of a method to regenerate complete individuals from the transformed cells. Somatic embryo cultures (23, 24) meet this requirement and offer an excellent starting point for genetic engineering. Cork oak somatic embryo cultures have low manipulation requirements, high proliferation rates, and plantlets can be obtained from embryogenic lines either initiated from zygotic embryos (25, 26) or induced in leaves from seedlings (27, 28). Desired traits are commonly expressed at maturity, so an effective selection can only be performed on mature trees. Perfectly fitted for this purpose, repetitive embryogenic lines can also be induced from mature individuals of this species (29, 30), opening the way to manipulation and cloning of desired genotypes. In fact, plants have been regenerated from several selected trees (31) and they do not seem to show significant differences with plants obtained from zygotic embryos (32). Moreover, genetic stability is a very valuable factor, and it has been shown that true-to-type plants can be obtained by somatic embryogenesis (33–35), and from cryopreserved embryogenic lines (36). Other recent advances in cork oak biotechnology include the use of anther culture to obtain haploid embryos (37) and the production of synthetic seeds (38). This chapter on cork oak genetic transformation follows a previous one (39), revised and updated accordingly to the findings in (6, 40, 41). Here, it is shown that transformation efficiencies (i.e., percentage of inoculated explants that yield independent transgenic embryogenic lines) of up to 43% can be obtained. Although still highly dependent on the genotype, which is a critical variable, correct choices of explant, cocultivation period, and inoculum density enable a significant improvement over the previous protocol. This chapter is focused on the genetic transformation step. However, the complete protocol is provided for convenience.

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From the collection of branches from a mature cork oak between December and May, to the transformed plantlet growing in the nursery, the protocol can be completed in about one and a half years. It involves the following: –

Collection of branches and induction of somatic embryogenesis: at least 4 months.

–

Proliferation until enough materials are obtained to start the transformation: at least 3 months.

–

Genetic transformation and selection of kanamycin-resistant lines: at least 4 months.

–

Proliferation until enough materials are obtained for the germination stage: at least 3 months.

–

Germination protocol: 3 months.

–

Plantlet establishment: 1 month.

2. Materials 2.1. Plant Materials

If you wish to obtain embryogenic lines from trees: branches of 1–4 cm in diameter from the crown of the selected Q. suber L. tree, cut preferably between December and May. If you are starting the transformation protocol straightaway: Q. suber L. somatic embryos and clusters from a cork oak embryogenic line (see Note 1).

2.2. Bacterial Strain and DNA Construct

AGL1 Agrobacterium tumefaciens strain (42) harboring a suitable plasmid with kanamycin resistance (see Notes 2 and 3).

2.3. Culture Media

If you wish to obtain embryogenic lines from trees: 1. Basic medium: microelements, vitamins, and Fe-EDTA from the MS medium (43). 2. Preconditioning medium (GMS): basic medium plus ½ PRL4-C macroelements [PRL-4-C (1×) contains 90 mg/L NaH2PO4·H2O, 30 mg/L Na2HPO4, 300 mg/L KCl, 200 mg/L (NH4)2SO4, 250 mg/L MgSO4·7H2O, 1000 mg/L KNO3, and 150 mg/L CaCl2·2H2O] (44), and 1% (w/v) sucrose. 3. Primary induction medium (MSSH1): basic medium plus SH macroelements [SH (1×) contains 2500 mg/L KNO3, 200 mg/L CaCl2·2H2O, 400 mg/L MgSO4·7H2O and 300 mg/L NH4H2PO4] (45), 3% (w/v) sucrose, 10 μM benzyladenine (BA), and 50 μM 1-naphthaleneacetic acid (NAA). 4. Secondary induction medium (MSSH2): basic medium plus SH macroelements, 3% (w/v) sucrose, 0.5 μM BA, and 0.5 μM NAA.

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5. Expression/proliferation medium (MSSH): basic medium plus SH macroelements and 3% (w/v) sucrose. The above-mentioned media (GMS, MSSH1, MSSH2, and MSSH) were pH-adjusted at 5.7 and 0.6% (w/v) agar added prior autoclaving at 120°C for 20 min. If you are starting the transformation protocol straightaway: 6. Expression/proliferation medium (MSSH): basic medium plus SH macroelements and 3% (w/v) sucrose, pH 5.7 and 0.6% (w/v) agar. 7. YEP medium [YEP (1×) contains 10 g/L bacteriological peptone, 5 g/L NaCl, and 10 g/L yeast extract. Adjust pH to 6.9] (46). Alternatively, Lysogeny Broth [LB; (1×) contains 10 g/L tryptone, 10 g/L NaCl, and 5 g/L yeast extract] can be used. Add 1.5% (w/v) agar for solid medium (store indefinitely at room temperature and always check the medium for contamination before use) (see Note 4). 8. Liquid MSSH medium. 9. Embryo maturation medium (see Subheading 3.6, Protocol 2, SOM medium): basic medium plus Sommer’s Medium 1 macroelements [Sommer’s M1 (1×) contains 200 mg/L (NH4)2SO4, 150 mg/L CaCl2·2H2O, 250 mg/L MgSO4·7H2O, 1000 mg/L KNO3, 300 mg/L KCl, 0.75 mg/L KI, 90 mg/L NaH2PO4·H2O, 30 mg/L NaHPO4] (47), 3% (w/v) sucrose, 1% activated charcoal, and 0.8% (w/v) agar, pH 5.6. 10. Embryo germination medium (Protocol 2, SOMG): SOM with sucrose concentration reduced to 1.5% (w/v), no activated charcoal, agar concentration increased to 1% (w/v) and supplemented with 0.22 μM BA and 0.50 μM indole-3-butyric acid (IBA). The above-mentioned media were pH-adjusted and then autoclaved at 120°C for 20 min. 2.4. Stock Solutions

2.4.1. Antibiotics (see Note 6)

If you wish to obtain embryogenic lines from trees: –

For the asepsia: fungicides (e.g., Propamocarb and Carbendazyme), 70% ethanol, commercial bleach, Tween 20, and sterile water.

–

Plant growth regulators: BA, NAA, and IBA (see Note 5).

1. Kanamycin (100 mg/mL stock in water, sterile filtrated. Store at −20°C). 2. Rifampicin (10 mg/mL stock in DMSO or methanol. Light sensitive. Store at −20°C). 3. Cefotaxime (250 mg/mL stock in water, sterile filtrated. This antibiotic is light and temperature sensitive. Store at −20°C).

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1. 10 mM MgSO4 (sterilize by autoclaving at 120°C for 20 min and store indefinitely at room temperature). 2. Activated charcoal, acid washed. If a β-glucuronidase assay is to be performed, prepare a buffer containing: 100 mM phosphate buffer 7.0 (see Note 7) 0.5 mM K3Fe(CN)6 0.5 mM K4Fe(CN)6 (see Note 8) 10 mM Na2EDTA 0.1% Triton X-100 1 mM 5-bromo-4-chloro-3-indolylglucuronide (X-Gluc) in dimethylformamide. Store at −20°C for up to a few weeks. Adjust to the final volume with water (see Note 9).

2.5. Other Supplies

1. 250-mL baby food jars or other appropriate containers for in vitro culture. 2. Sterile consumables: 60- and 90-mm Petri dishes, 50-mL centrifuge tubes, and filter paper (see Note 10). 3. Parafilm®. 4. Sterile water. 5. Forest containers (180 mL, Arnabat SA, Spain) (see Note 11). 6. Substrate: pine bark–peat–sand 3:1:1 (v/v/v). 7. REDExtract-N-AmpTM Plant PCR Kit (Sigma®; see Note 12). 8. DNeasy® Plant Mini Kit for DNA isolation from plant tissue (Quiagen®; see Note 13). 9. Primers:

Gene nptII

Reverse primer (5¢–3¢)

V00618.1 GAGGCTA TTCGGC TATGACTG

ATCGGGAGC GGCGATAC CGTA

700

GTTTACGC GTTGCTTC CGCCA

1,199

ATCTCAA GCCCA TCTTCACG

199

uidA- – PIV2 virG

Amplified fragment (bp)

Forward primer GenBank (5¢–3¢)

GGTGGGA AAGCGC GTTACAAG

X62885.1 AAGGTGA GCCGTT GAAACAC

10. Laboratory equipment, including the following: water purification system, autoclave, tabletop centrifuge (capable of spinning 50 mL tubes at 3,000 × g), flow hood, culture chamber

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(illumination of 120–180 μmol/m2 s), sterile equipment (scalpels and forceps), 30°C oven, orbital shaker (capable of keeping a temperature below 30°C), PCR thermocycler, and agarose gel electrophoresis equipment.

3. Methods 3.1. Induction of Embryogenesis in Leaves from Adult Q. suber

For a more complete description of this protocol, or if you wished to induce embryogenesis in zygotic embryos or leaves from seedlings, please see the original references (30, 48). 1. Cut 1–4 cm diameter branches from the crown of the selected tree, preferably between December and May. Remove lateral branches and leaves, washing and brushing thoroughly, and culture segments up to 15 cm long in a perlite substrate in appropriate available containers (e.g., 5,000 cm3) at 25 ± 5°C and 80–95% relative humidity in a greenhouse or climatic chamber. Spray them weekly with fungicides (e.g., 1.8 g/L Propamocarb and 60% Carbendazyme) to prevent fungal infections. 2. Collect the expanding leaves (0.5–1.5 cm from the base to the apex) with small petioles from the growing epicormic shoots (see Fig. 1a) and surface-sterilize them by vigorously handshaking in 70% (v/v) ethanol for 30 s. Transfer them to 10% commercial bleach (3.5% active chlorine) plus two drops of Tween 20 for 10 min, preferably on a magnetic stirrer (see Note 14). Finally, rinse them three times with sterile distilled water. 3. Place two surface-sterilized leaves with the abaxial surface on GMS in each 60-mm Petri dish, seal it with Parafilm, and culture at 25°C in the dark for 7 days. 4. Transfer the leaves to the MSSH1 and incubate in the dark at 25°C for 30 days. 5. Transfer the leaves to the MSSH2 and incubate in a 16-h photoperiod (mixed Sylvania Gro-Lux and Philips cool white fluorescent tubes, 120–180 μmol/m2·s) at 25°C for 30 days. 6. Transfer the leaves onto MSSH and subculture every 30 days in the conditions of the previous step until embryo clusters appear (see Fig. 1b). 7. Isolate embryo clusters and keep on subculturing them without changing the conditions every 20–40 days. The shorter the subculture period, the faster the growth and the lower the number of embryos that will reach maturity.

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Fig. 1. Stages of the transformation procedure. (a) Epicormic shoots with leaves, sprouted in a fragment of branch in perlite substrate. (b) Somatic embryogenesis induction on a treated expanding leaf. The somatic embryos spontaneously undergo secondary embryogenesis. Bar, 4 mm. (c) Cotyledonary embryo (left ) and cluster of embryos in early stages of development (right ). Bar, 1 mm. (d) White putatively transformed embryo mass, proliferating on a necrotic cluster in presence of kanamycin. (e) Appearance of an embryo selected to be cold-treated. Bar, 4 mm. (f) Germinated somatic embryo. (g) Cork oak plantlet growing in field conditions. Partially reproduced from (55) with kind permission from Springer.

3.2. Bacterial Strain Culture and Preparation

1. Streak the −80°C preserved Agrobacterium strain on agar-YEP with 100 mg/L kanamycin and 20 mg/L rifampicin in the dark at 28°C for 2–3 days (these cultures can be stored for up to a month at 4°C, see Notes 6 and 15). 2. Pick an isolated colony and grow it overnight in liquid YEP with 50 mg/L kanamycin in an orbital shaker at 28°C and 250 rpm (see Note 16). 3. Measure the OD600 of the culture and take the necessary amount to prepare 20 mL of a final OD600 of 1 (see Note 17).

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4. Pellet the bacteria (3,000 × g for 10 min) and resuspend the pellet in 10 mL of 10 mM MgSO4. 5. Pellet again and resuspend to a final OD600 of 1 in liquid MSSH medium. 3.3. Preculture, Inoculation, and Coculture of the Embryo Clusters

1. Collect embryo clusters (see Fig. 1c) 20 days after the last subculture (see Note 18). Do it in liquid MSSH to prevent desiccation. 2. Halve the clusters with a scalpel and inoculate them with the bacteria–MSSH solution for 20 min with gently shaking (e.g., up to 100 rpm in an orbital shaker) (see Notes 17 and 19). 3. Blot the embryos on sterile filter paper to eliminate excess of bacteria and transfer them (20–30 embryos per Petri dish) to solid MSSH medium without antibiotics. 4. Coculture for 2 days at 25°C in the dark (see Note 20). 5. Wash the embryos in liquid MSSH medium with 500 mg/L cefotaxime to eliminate excess of bacteria, blot on sterile filter paper and transfer them (10–15 embryos per baby food jar) to MSSH medium with 100 mg/L kanamycin and 500 mg/L cefotaxime (see Note 21).

3.4. Selection of Transformed Embryogenic Lines

1. Subculture the inoculated and washed embryos in MSSH medium with 100 mg/L kanamycin and 500 mg/L cefotaxime (selective medium) every 7–10 days for the first month, and at 15–20 day intervals thereafter. Keep the cultures at 25 ± 1°C under a 16-h photoperiod (see Note 22). 2. Isolate white proliferating embryogenic masses emerging from the initial explants (see Fig. 1d) and keep on subculturing them on selective medium for about three more months (see Note 23). 3. As soon as you have enough material, check the selected explants for the presence of nptII, your gene of interest and the Agrobacterium helper plasmid gene (virG) by PCR or southern blot. Then check for the expression of your gene of interest by reverse-transcription PCR, northern blot or a histochemical assay (see next section and Note 24). 4. Maintain the kanamycin-resistant embryogenic masses by subculturing them on proliferation (MSSH) medium without antibiotics in standard conditions (25 ± 1°C and 16-h photoperiod) every 20–40 days.

3.5. Molecular and Histochemical Analyses

For PCR, the DNA can be extracted using either the REDExtractN-AmpTM Plant PCR Kit from Sigma® or a standard procedure. For southern blot, the DNA can be extracted and purified using the DNeasy® Plant Mini Kit for DNA isolation from plant tissue (Quiagen®) or a standard procedure (see Note 13).

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1. Both uidA and nptII genes can be amplified in the same PCR tube in the following conditions: 4 min 95°C, 35x(20 s 95°C, 30 s 58°C, 60 s 72°C), 5 min 72°C. 2. PCR conditions for virG: 4 min 95°C, 35x(20 s 95°C, 30 s 56°C, 15 s 72°C), 5 min 72°C.

3.5.2. Southern Blot Analysis

Southern blot analyses (4, 49) should be performed to confirm the stable integration of the transgenes.

3.5.3. Histochemical (b-glucuronidase) Analysis of Transformants

If a uidA-harboring plasmid such as the pBINUbiGUSint is used, a β-glucuronidase assay can be performed to assess protein functionality. To do so: 1. Take embryos proliferating in presence of kanamycin, not exceeding 2–3 mm in size. 2. Incubate them in the dark at 37°C for at least 2 h (see Note 25) in the solution of GUS buffer plus X-Gluc (50). After transgene integration has been confirmed, expression should be assessed by RT-PCR or northern blot. For standard procedures see (49).

3.6. Embryo Germination 3.6.1. Protocol 1 (Extracted from (31, 48))

1. Select embryos that undergo spontaneous maturation (white opaque, 15–20 mm in length, average fresh weight of 225 mg and without signs of secondary embryogenesis, see Fig. 1e) and transfer them to fresh MSSH medium. 2. Cold store the cultures in the dark at 4°C for 2 months. 3. Transfer the cultures to 16-h photoperiod (100 μmol/m2·s) at 25°C. About 15 days after, they will start germinating (see Fig. 1f).

3.6.2. Protocol 2 (Extracted from (41))

1. Select immature translucent embryos at the cotyledonary stage (about 3–4 mm long and 30 mg fresh weight). 2. Culture the embryos in 90-mm Petri dishes containing 25 mL SOM medium for 1 month at 25°C in the dark. 3. When they are about 1.5–2 cm long and 700–1,000 mg fresh weight, transfer them to fresh SOM and store the cultures for 2 months at 4°C in the dark. 4. After the cold stratification, imbibe the embryos in 10-mL tubes with sterile distilled water for 24 h in the dark. 5. Germinate the embryos in SOMG medium at 25°C in a 16-h photoperiod (100 μmol/m2 s).

3.7. Plant Conversion

1. Once germinated, transfer the embryos to 180-mL forest containers filled with pine bark–peat–sand 3:1:1 (v/v/v) substrate (see Note 26). Cover them with inverted glass beakers and

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keep them in the growth chamber (alternatively you can keep them in a chamber with a fog system, gradually reducing the humidity for a month before transferring the plants to the nursery). 2. After 2 months, remove the beakers for 1 h/day for 1 month. 3. Move the plants to the nursery, under shade (see Fig. 1g).

4. Notes 1. Our research suggests that the parental tree genotype strongly influences transformation efficiency (6). The embryogenic lines with lower proliferation efficiency were less transformation-responsive. We suggest that a treatment to increase the proliferation rate would likely increase the transformation competence of these lines as well. 2. Our research suggests that the A. tumefaciens strain strongly influences transformation efficiency (4). 3. Have your gene of interest sequenced from the final construct. A size confirmation by PCR is not safe enough, since the cloned gene may have mutations that could produce aberrant proteins. Therefore, make sure you start this lengthy transformation protocol with the right construct. We have successfully used the pBINUbiGUSint binary vector (51) to transform explants with the uidA gene (6), and the pBINUbiBar to introduce herbicide resistance with the bar gene in cork oak (40). Both plasmids are derivatives of pBIN19 (52) and carry the neomycin phosphotransferase II gene (nptII), which confers resistance to kanamycin. Hygromycin resistance has also been successfully used to obtain cork oak transgenic embryogenic lines (5). 4. The smaller the agar-media stocks, the lower the time required to melt and thaw them. Therefore, 50–200 mL stocks are recommended. Melt the medium in a microwave oven, cool the medium down till about 50°C (at this temperature it can be held with bare hands) and then add the appropriate sterile-filtered antibiotics. 5. Prepare the plant growth regulators as 1 mg/mL stocks. Dissolve the powder in NaOH 1 M (no more than 5% of the final volume), dilute them with milliQ water up to the final volume, sterile-filter, and transfer them to either Pyrex glass or plastic. If you store them in regular glass, you will probably observe silicate precipitates after a few days or weeks due to the presence of NaOH. Store in the fridge for a few weeks or at

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−20°C for a few months (indole-3-butyric acid liquid stocks should be always stored below 0°C). In the original articles, plant growth regulators are added before autoclaving. 6. You can store the antibiotics as 1-mL aliquots. The AGL1 Agrobacterium strain has a chromosomal resistance to rifampicin and carbenicillin, and the pBINUbiGUSint plasmid confers resistance to kanamycin. Carbenicillin resistance confers cross-resistance to ticarcillin (both of them are beta-lactam antibiotics), so the latter will not effectively eliminate AGL1 from the cultures. Cefotaxime is a cephalosporin antibiotic with bacteriostatic properties which can be used to eliminate AGL1. 7. The phosphate buffer pH 7 can be prepared by adding 61 mL of 200 mM Na2HPO4 (weak base) to 39 mL of 200 mM NaH2PO4 (weak acid). If the pH is not right, it can be adjusted with either the weak base or the weak acid. Store these stocks at room temperature and sterile-filter to avoid precipitation and contamination. 8. These cyanides are catalysts. If you do not add them to the buffer you may obtain false positives due to the activity of cell peroxidases. For convenience, prepare them separately as 50 mM stocks in water and store refrigerated in the dark. 9. X-Gluc can be prepared separately as a 20 mM stock, and both X-Gluc and buffer stored at −20°C for up to a few weeks. Just mix them before use to make up the right concentrations. Large GUS assays can be conveniently performed and screened, e.g., in 96-well plates. 10. Sterilize filter paper by autoclaving instead of using an oven (100–150°C). After some time in the oven the paper starts scorching, turns brittle, and loses its ability to absorb water. In addition, phenols are produced when scorching and can interfere with the cultures. 11. Square-section forest containers are better than their circlesection counterparts. Roots grow straight to the bottom in the square containers, but in spiral manner along the container wall in the circular ones. The straight-growing roots provide higher conversion rates (% survival of greenhouse plants when transferred to field), since a coiled root system usually cannot support the weight of the aerial part and the plant is more prone to fall down. 12. The Sigma® REDExtract-N-AmpTM Plant PCR is a convenient and low-cost kit. It provides DNA extraction buffers and PCRmix (Taq polymerase plus buffer, dNTPs, and MgCl2), and no DNA purification is needed. If a classical PCR reaction is preferred, extract or purify DNA with an appropriate method (e.g., (53)) and set up a PCR reaction containing DNA

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(100 ng), 250 μM of each dNTP, 10 pmol of each primer, Taq DNA polymerase, and 2 mM MgCl2. 13. For southern analysis, purification of the DNA is required for the digestion with restriction enzymes to work well. Ten micrograms of DNA can be easily obtained with the DNeasy® Plant Mini Kit for DNA isolation from plant tissue (Quiagen®) starting from 100 mg of embryogenic tissue (fresh weight). If a column-based kit is not available a CTAB-based DNA purification protocol is recommended, as a phenol-based one would probably work poorly due to the high carbohydrate content of the embryos. Pick up clusters or embryos in early stages of development, since cotyledonary embryos consist of highly vacuolated cells that can result in a poor DNA extraction rate. 14. The shake-in-ethanol step kills some microorganisms and removes mainly waxes and dust, facilitating the bleaching that follows. Stirring or shaking is strongly recommended as it improves the efficiency of the asepsia by removing bubbles and brushing the leaf surface. Do not increase stirring speed until a vortex is formed because air bubbles hinder the asepsia; just keep the leaves in a reasonable motion. 15. Agrobacteria strains can be cryopreserved and maintained at −80°C for about 10 years. To do so, grow bacteria to the exponential phase (OD600 ~ 0.4), spin, redissolve the pellet in 0.5 mL of sterile YEP with 15% glycerol in suitable tubes, and flashfreeze in liquid nitrogen. If you do not flash-freeze them their viability will be reduced, but they will still be fine for a few years at −80°C. For short-term preservation up to a few months, pick a colony and stab it in a microcentrifuge tube with 1 mL of sterile agar-YEP. Keep this so-called “stab culture” at room temperature or in the fridge. 16. Cultures require 16–24 h to grow in 20–30 mL of YEP medium. If the bacteria have been for some time in the fridge, it is recommended to start a preinoculum in 1 mL of medium without antibiotics, which after 4–8 h is diluted with medium with 50 mg/L kanamycin. 17. 20 mL of bacterial suspension are enough to inoculate 100– 150 embryo clusters in a 50-mL sterile tube. 10 mL (2× OD600) of bacterial suspension can be used and mixed with the 10 mL of liquid MSSH employed to gather the embryos while they are collected. By doing this, phenols released by the embryos could induce bacterial vir genes. Inoculum density is an important factor (6), but the density could be reduced to OD600 = 0.5 if bacterial regrowth after coculturing is too persistent. 18. The 20-day preculture period is a key factor (6). A preculture longer than 27 days is likely to result in poor transformation efficiencies.

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19. Collection can be performed while preparing bacteria, saving time. Shaking rates above 100 rpm can result in damage for the embryos. 20. Although a cocultivation at 22°C yielded the highest transformation efficiency, the temperature in the range of 22–26°C did not significantly affect this efficiency. Moreover, a cocultivation period longer than 2 days significantly reduced the efficiency (6). Interestingly, vir gene induction is maximal at 25–27°C, while the pilus of some Agrobacterium strains is most stable at lower temperatures (18–20°C) and unstable over 28°C (references in (54)). Coculturing in the light might affect the transformation efficiency (Alvarez et al. unpublished results). 21. This step is strongly recommended. We have observed that the embryos looked healthier during the subsequent subculture periods when they were washed to eliminate excessive Agrobacterium. More importantly, this step reduces the number of explants that suffer bacterial regrowth. Given that embryogenic clusters are irregularly shaped, vacuum infiltration of antibiotics could be performed to improve elimination of bacteria. 22. Cefotaxime is photo- and thermolabile; therefore, frequent subculture is recommended to avoid regrowth of bacteria. As commented in (30), embryos grow irrespective of the light conditions, so culturing them in dim light or darkness is also a good option to mitigate cefotaxime activity loss. Picking and discarding dead cotyledons is a good practice, since bacteria usually regrow on them. 23. This continuous subculture in selective medium allows obtaining nonchimeric cultures (4). 24. Bear in mind that presence of a gene does not always imply expression. If your transgenic plant shows no phenotype, this might mean for instance that the gene has been silenced or that it is truncated and therefore not expressed correctly. 25. Whitish embryos that have grown in the dark are the preferred samples for a GUS assay. Under light conditions some embryos become green or develop black necrotic areas, which can be misleading when trying to see blue spots. Blue staining appears usually within 4 h of incubation, but overnight incubations can be required for instance in transient expression analysis, since the GUS spots will be very small. A low vacuum can be applied to facilitate penetration of the X-Gluc into the embryos. The smaller the samples, the faster the staining. 26. Do not wait for the radicle to elongate too much before the transfer, since this reduces conversion rates.

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References 1. FAO (2004) Preliminary review of biotechnology in forestry, including genetic modification. Forest Genetic Resources Working Paper FGR/59E. Forest Resources Development Service, Forest Resources Division. Rome, Italy 2. Boerjan W (2005) Biotechnology and the domestication of forest trees. Curr Opin Biotechnol 16:159–166 3. Merkle SA et al (2007) Restoration of threatened species: a noble cause for transgenic trees. Tree Genet Genomes 3:111–118 4. Álvarez R et al (2004) Genetic transformation of selected mature cork oak (Quercus suber L.) trees. Plant Cell Rep 23:218–223 5. Sánchez N et al (2005) Agrobacteriummediated transformation of cork oak (Quercus suber L.) somatic embryos. New For 29:169–176 6. Álvarez R, Ordás RJ (2007) Improved genetic transformation protocol for cork oak (Quercus suber L.). Plant Cell Tiss Organ Cult 91:45–52 7. Carraway DT et al (1994) Somatic embryogenesis and gene transfer in American chestnut. J Am Chestnut Found 8:29–33 8. Fernando DD et al (2006) In vitro germination and transient GFP expression of American chestnut (Castanea dentata) pollen. Plant Cell Rep 25:450–456 9. Polin LD et al (2006) Agrobacterium-mediated transformation of American chestnut (Castanea dentata (Marsh.) Borkh.) somatic embryos. Plant Cell Tiss Organ Cult 84:69–79 10. Rothrock RE et al (2007) Plate flooding as an alternative Agrobacterium-mediated transformation method for American chestnut somatic embryos. Plant Cell Tiss Organ Cult 88:93–99 11. Andrade GM et al (2009) Sexually mature transgenic American chestnut trees via embryogenic suspension-based transformation. Plant Cell Rep 28:1385–1397 12. Seabra R, Pais MS (1998) Genetic transformation of European chestnut. Plant Cell Rep 17:177–182 13. Seabra R, Pais MS (1999) Genetic transformation of European chestnut (Castanea sativa Mill.) with genes of interest. Acta Hort (ISHS) 494:407–414 14. Corredoira E et al (2004) Agrobacteriummediated transformation of European chestnut embryogenic cultures. Plant Cell Rep 23: 311–318

15. Corredoira E et al (2006) Genetic transformation of Castanea sativa Mill. by Agrobacterium tumefaciens. Acta Hort (ISHS) 693:387–394 16. Corredoira E et al (2007) Improving genetic transformation of European chestnut and cryopreservation of transgenic lines. Plant Cell Tiss Organ Cult 91:281–288 17. Caro LA et al (2003) Agrobacterium rhizogenes vs auxinic induction for in vitro rhizogenesis of Prosopis chilensis and Nothofagus alpina. Biocell 27:311–318 18. Roest S et al (1991) Agrobacterium-mediated transformation of oak (Quercus robur L.). Acta Hort (ISHS) 289:259–260 19. Wilhelm E et al (1996) Plantlet regeneration via somatic embryogenesis and investigations on Agrobacterium tumefaciens mediated transformation of oak (Quercus robur). In: Ahuja MR, Boerjan W, Neale DB (eds) Somatic cell genetics and molecular genetics of trees. Kluwer Academic Publishers, Dordrecht 20. Vidal N et al (2010) Regeneration of transgenic plants by Agrobacterium-mediated transformation of somatic embryos of juvenile and mature Quercus robur. Plant Cell Rep 29:1411–1422 21. Aronson J et al (2009) Cork oak woodlands on the edge: ecology, adaptive management, and restoration. Island, Washington, DC 22. Paleo UF (2010) The dehesa/montado landscape. In: Bélair C, Ichikawa K, Wong BYL, Mulongoy KJ (eds). Secretariat of the Convention on Biological Diversity, Montreal. Technical Series No 52 23. Neumann KH (2006) Some studies on somatic embryogenesis: a tool in plant biotechnology. In: Sopory SK, Roy S, Kumar A (eds) Plant biotechnology. IK International Publishing House Pvt Ltd, New Delhi 24. Rose RJ et al (2010) Developmental biology of somatic embryogenesis. In: Pua EC, Davey MR (eds) Plant developmental biology Biotechnological perspectives. Springer, Berlin 25. Bueno MA et al (1992) Plant regeneration through somatic embryogenesis in Quercus suber. Physiol Plant 85:30–34 26. Manzanera J et al (1993) Somatic embryo induction and germination in Quercus suber L. Silvae Genet 42:90–93 27. Fernández-Guijarro B et al (1994) Somatic embryogenesis in Quercus suber L. In: Pardos JA, Ahuja MR, Elena-Rossello R (eds) Investigación Agraria, Sistemas y Recursos Forestales. INIA, Madrid

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28. Fernández-Guijarro B et al (1995) Influence of external factors on secondary embryogenesis and germination in somatic embryos from leaves of Quercus suber L. Plant Cell Tiss Organ Cult 41:99–106 29. Hernández I et al (2001) Cloning mature cork oak (Quercus suber L.) trees by somatic embryogenesis. Melhoramento 37:50–57 30. Hernández I et al (2003) Vegetative propagation of Quercus suber L. by somatic embryogenesis. I. Factors affecting the induction in leaves from mature cork oak trees. Plant Cell Rep 21:759–764 31. Hernández I et al (2003) Vegetative propagation of Quercus suber L. by somatic embryogenesis. II. Plant regeneration from selected cork oak trees. Plant Cell Rep 21:765–770 32. Hernández I et al (2009) Growth data from a field trial of Quercus suber plants regenerated from selected trees and from their half-sib progenies by somatic embryogenesis. Acta Hort (ISHS) 812:493–498 33. Loureiro J et al (2005) Assessment of ploidy stability of the somatic embryogenesis process in Quercus suber L. using flow cytometry. Planta 221:815–822 34. Lopes T et al (2006) Determination of genetic stability in long-term somatic embryogenic cultures and derived plantlets of cork oak using microsatellite markers. Tree Physiol 26:1145–1152 35. Valladares S et al (2006) Plant regeneration through somatic embryogenesis from tissues of mature oak trees: true-to-type conformity of plantlets by RAPD analysis. Plant Cell Rep 25:879–886 36. Fernandes P et al (2008) Cryopreservation of Quercus suber somatic embryos by encapsulation-dehydration and evaluation of genetic stability. Tree Physiol 28:1841–1850 37. Pintos B et al (2007) Antimitotic agents increase the production of doubled-haploid embryos from cork oak anther culture. J Plant Physiol 164:1595–1604 38. Pintos B et al (2008) Synthetic seed production from encapsulated somatic embryos of cork oak (Quercus suber L.) and automated growth monitoring. Plant Cell Tiss Organ Cult 95:217–225 39. Álvarez R et al (2007) Cork oak trees (Quercus suber L.). In: Wang K (ed) Agrobacterium protocols, Volume II. Humana, Totowa 40. Álvarez R et al (2009) Genetic transformation of cork oak (Quercus suber L.) for herbicide resistance. Biotechnol Lett 31:1477–1483 41. Pintos B et al (2010) Oak somatic and gametic embryos maturation is affected by charcoal and

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44.

45.

46.

47.

48.

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50.

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52.

53.

54.

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specific aminoacids mixture. Ann For Sci 67:205 Lazo GR et al (1991) A DNA transformationcompetent Arabidopsis genomic library in Agrobacterium. Bio/Technology 9:963–967 Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497 Gamborg OL (1966) Aromatic metabolism in plants. II. Enzymes of the shikimate pathway in suspension cultures of plant cells. Biochem Cell Biol 44:791–799 Schenk RU, Hildebrandt AC (1972) Medium and techniques for induction and growth of monocotyledonous and dicotyledonous plant cell cultures. Can J Bot 50:199–204 An G et al (1988) Binary vectors. In: Gelvin SB, Schilperoort RA, Verma DPS (eds) Plant molecular biology manual. Kluwer Academic Publishers, Dordrecht Sommer HE et al (1975) Differentiation of plantlets in longleaf pine (Pinus palustris Mill.) tissue cultured in vitro. Bot Gaz 136:196–200 Toribio M et al (2005) Cork oak, Quercus suber L. In: Jain SM, Gupta PK (eds) Protocol for somatic embryogenesis in woody plants. Springer, Dordrecht Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY Jefferson RA (1987) Assaying chimeric genes in plants: the GUS gene system. Plant Mol Biol Rep 5:387–405 Humara J et al (1999) Improved efficiency of uidA gene transfer in stone pine (Pinus pinea) cotyledons using a modified binary vector. Can J For Res 29:1627–1632 Bevan M (1984) Binary Agrobacterium vectors for plant transformation. Nucleic Acids Res 12:8711–8721 Berendzen K et al (2005) A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thaliana ecotypes Col-0 and Landsberg erecta. Plant Methods 1:4 Gelvin SB (2003) Agrobacterium-mediated plant transformation: the biology behind the “gene-jockeying” tool. Microbiol Mol Biol R 67:16–37 Álvarez R et al (2007) Agrobacterium protocols volume 2 Cork oak trees (Quercus suber L.). Springer, New York, NY

Chapter 29 Organelle Transformation Anjanabha Bhattacharya, Anish Kumar, Nirali Desai, and Seema Parikh Abstract The source of genetic information in a plant cell is contained in nucleus, plastids, and mitochondria. Organelle transformation is getting a lot of attention nowadays because of its superior performance over the conventional and most commonly used nuclear transformation for obtaining transgenic lines. Absence of gene silencing, strong predictable transgene expression, and its application in molecular pharming, both in pharmaceutical and nutraceuticals, are some of many advantages. Other important benefits of utilizing this technology include the absence of transgene flow, as organelles are maternally inherited. This may increase the acceptability of organelle transformation technology in the development of transgenic crops in a wider scale all over the globe. As the need for crop productivity and therapeutic compounds increases, organelle transformation may be able to bridge the gap, thereby having a definite promise for the future. Key words: Organelle transformation, Plastids, Biolistics, Gene expression

1. Introduction Even after quite a few decades of successful production of transgenic crops, several countries are still skeptical about the final outcome or long-term effects of transgenic crops or, more specifically, transgenes. The perceived threat is with the outflow of transgenes in the environment, thereby contaminating crops. At the same time, with the ever-increasing pressure on land, climate change, and the need to feed the ever-increasing human populations and their livestock, there is an increasing demand towards developing crop varieties which can sustain on minimal inputs, survive in extremities of climate, disease, and pest infestation, and yet produce higher yield. Again, the burning issue of food versus fuel has added pressure to our limited resources to increase and sustain food production. Most of the concern against GM technology pertains to regulation of

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_29, © Springer Science+Business Media, LLC 2012

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transgene activity, gene flow across species and gene contamination, and as such. However, nuclear transformation has several drawbacks including, but not restricted to, unpredictable expression of gene of interest and gene silencing (1, 2). This has restricted the acceptance of transgenic technology and a number of trails have to be done before release of a particular variety. Sometimes described as good management practices, it costs millions of dollars to get to the approval process. This led researchers to look beyond nuclear transformation, the method of choice until now. Finally, scientists looked at other organelle within the plant cell for developing effective transformation strategy (3). The mitochondria and chloroplast became the targets of choice. Briefly, during the evolution of land plants, chloroplast had an independent existence, as prokaryotic organism (4). Somehow, a symbiosis was established over millions of years of evolution of early primitive plants and chloroplasts, which finally may have led to loss of several genes from the chloroplast genome, which typically changed from parasitic to symbiotic mode, required for independent existence (5). Thus, the chloroplast became part and parcel of cell. The same theory has been hypothesized for mitochondria. The only limitation is that nongreen cells do not contain chloroplast. This is where mitochondrial transformation is of importance. Further, plastids can be categorized as chloroplast, chromoplast, and amyloplast behind several others (6). 1.1. Chloroplast Transformation

The chloroplast genome is comparatively very small, 150 kb on an average, and is normally similar across species, compared to the nuclear genome, 125 Mb in Arabidopsis to about 2,800 Mb in sugarcane. Chloroplast genome replicates independently of the nuclear genome. Chloroplast genome is of prokaryotic origin and circular in nature. Therefore, specific constructs are prepared with the gene of interest and flanking regions similar to chloroplast genome are included, specific for specific crops (7, 8). When the construct is delivered to the plant cell, these flanking regions guide the gene of interest to the exact place within the chloroplast genome, and thereby targeted delivery of genes can be done (8). This results in enhanced expression of transgene, avoidance of intregration of multiple copies of gene of interest, and as such. Besides, chloroplasts are inherited maternally and therefore, transgene escape is avoided.

1.2. Mitochondria Transformation

Unlike chloroplast transformation, mitochondria have not been exploited to that extent. There are only a few thematically published papers like those of (9–11) on this subject. Till date, there is hardly any report that proved commercial application of such technology. Mitochondria genome is about 1,800 kbp, which is ten times larger than chloroplast genome but very small compared to nuclear genome. Hopefully, in the coming years, mitochondria transformation technology will be fine-tuned to suit for a variety of crops.

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2. Illustration of the Method 2.1. Overview 2.1.1. Bioinformatics

2.1.2. Cloning the Gene of Interest

Flanking regions suitable for any chloroplast transformation experiment from the chloroplast genome database should be identified from the freely available gene data available at NCBI, AtESEMBL, and as such. Please note that several researches have noted that cross-species flanking regions do not work properly on several occasions when performing chloroplast transformation (6). On this note, as demand for DNA sequencing increased, new technologies were invented to reduce cost and the time involved and increase reliability. From the traditional Sanger sequencing that could read 70 kbp per run, sequencing technologies have revolutionized to the modern-day Illumina sequencing (Solexa) or AB gene (SOliD) instrument which can read up to 3 Gbp reads per run. These have set the stage for low-cost rapid sequencing techniques with greater coverage for other cultivated crop species beyond the scope of first-generation sequenced model crop plants and that fasten the pace for trait discovery. So, in the coming years, many more chloroplasts from several crop species will be sequenced from the current 40 crops species and contribute towards developing better constructs for chloroplast transformation. Let us say, we have a gene A, which we want to express and obtain a certain compound, say B. Therefore, we have to express A in an organism, say plant’s chloroplast. In order to do so, we have to find machinery, which will produce the gene in multiple copies and then we can use the construct (Vector + Insert) to transform a plant, i.e., chloroplast. (a) The gene of interest is PCR amplified or isolated and inserted into circular DNA molecule (Vector) which involves cutting the molecule at specific point using suitable restriction enzymes, confirming DNA (product) size, ligating the fragment to the vector, multiplication in E. coli, and restriction digest to confirm the size of the insert. Now, the resultant construct is a hybrid/chimera containing the gene as an insert. The gene is said to be cloned. (b) This construct carrying the cloned gene is used to transfer the Insert (which is the gene of interest) into the target organism. (c) Before doing so, it is essential to transfer the construct into a bacterium, which can make multiple copies.

2.2. Biolistics

For biolistics transformation, most constructs will work. Unlike Agrobacterium-mediated transformation, cross-species incompatibility of plasmids is not a problem with biolistics. The target gene is coated on to gold particles and fired into the plant cell (refer standard protocol). The transformed cells will regenerate in a

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suitable antibiotic media, which helps to kill or suppress the growth of nontransformed cells, thus differentially helping to enhance the growth of transformed cells only (see Note 1). Few points to be noted for particle preparation: Please take proper advice, care, and precautions before conducting experiments. Avoid contamination during the whole process. Key points 1. Take 60 mg of 0.6–1.0-μm gold particles, (this holds good for 120 bombardments), and vortex with 1 mL 100% ETOH. Repeat four times. 2. Centrifuge and remove supernatant. Add 1 mL sterile water (dH2O) and resuspend in sterile water. Wash twice with 1 mL sterile water. This preparation can be kept for up to 1 month at 4°C. This is good for 120 bombardments (500 ng gold/shot). However, we have seen that reducing gold concentration to 50 ng per shot did not bring about any drastic change in gfp expression in optimization trials. Vary plasmid DNA concentration 75–750 ng/shot. Optimization of protocol for specific experiments must be made for each new crop and variety. 3. For coating DNA, use 2.5 M CaCl2 (can be stored at −20°C for 6 months) and 0.1 M spermidine (prepare fresh or once prepared, store aliquot into 0.5-mL Eppondorf tubes at −20°C for about a month at the most and use each vial only once, i.e., once thawed, discard vial) as described in the Bio-Rad protocol. 4. Bombardment pressure: 1,800 psi or as applicable (adjust) to particular experiments. Distance between the sample platform and launch assembly: 5 cm; but we have found that 5 cm works better than 8 or 11 cm. This will vary between experiments. 5. Tissue culture protocol and explant type depend on particular crop and species. Generally, green callus is the preferred type for delivering transgene through chloroplast transformation (see Fig. 1).

3. Conclusion Organelle transformation, i.e., chloroplast transformation, provides new venues for enhancing crop production. Briefly, low copy number of genes in the chloroplast and presence of several origin of replication make it an attractive target for genetic engineering. Plant breeding alone is not able to deliver the goal of increased and sustained crop production. Today, GM crops are being grown in increasing acreage year after year across different countries and it is evident that GM technology will regain its lost status in the coming

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Fig. 1. Simplified representation of plastid transformation. The gold particles are coated with DNA and fired in the chloroplast using gene gun. The flanking sequences help to direct the DNA in order to integrate at specific position in the circular DNA of the chloroplast.

years. Chloroplast transformation technology provides viable clean GM technology. There are several advantages of adopting chloroplast transformation as chloroplast divides independent of the nucleus and precision genetic combination by targeted homologous combination at specified sites is a possibility, thus enhancing the value of chloroplast transformation. With many more plastids being sequenced nowadays, large amount of data is available for data mining and developing new flanking regions (12). Organelle transformation is superior to nuclear transformation because of trans-silencing, stable transformation, absence of cis-, high level of directed gene expression, and absence of transgene flow (13). However, organelle transformation is still in infancy and better approach must be taken to increase the efficiency of transformation in a wide variety of crops, particularly those that are recalcitrant to transformation (14, 15).

4. Note 1. Please refer standard Bio-Rad protocol for sample preparation and Gene gun operation. Please ensure that all safety measures are taken into consideration. The authors are not responsible for any situation arising thereof.

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Disclaimer Protocols described in this chapter are merely for descriptive purposes and we have no affiliation with any company including Bio-Rad for any commercial interest. The readers/users should read the user manual by manufacturer carefully and discuss all the procedures with experts/trained personnel before using any instruments or conducting any experiment. The readers will indemnify the contributors against any costs, expenses, or damages that may incur or for which contributors may become liable as a result of breach. These representations and warranties hold good for third parties also. References 1. Daniell H (2007) Transgene containment by maternal inheritance: effective or elusive? Proc Natl Acad Sci USA 17:6879–6880 2. Maliga P (2004) Plastid transformation in higher plants. Annu Rev Plant Biol 55: 289–313 3. Ishida K (2005) Protein targeting into plastids: a key to understanding the symbiogenetic acquisitions of plastids. J Plant Res 118: 237–245 4. Bhattacharya D et al (2007) How do endosymbionts become organelles? Understanding early events in plastid evolution. Bioassays 29: 1239–1246 5. Pyke PA (2007) Plastid development and differentiation. In: Bock R (ed) Topics in current genetics: plastid development. Springer, New York 6. Bhattacharya A (2010) Organelle transformation. In: Chittaranjan K, Michler CH, Abbott AG, Hall TC (eds) Transgenic crop plants, volume 1, principles and development. Springer-Verlag, Heidelberg 7. Hou BK et al (2003) Chloroplast transformation in oilseed rape. Transgenic Res 12: 111–114

8. Davarpanah SJ et al (2009) Stable plastid transformation in Nicotiana benthamiana. J Plant Biol 52:244–250 9. Weber-Lotfi F et al (2009) Developing a genetic approach to investigate the mechanism of mitochondrial competence for DNA import. Biochim Biophys Acta 1787:320–327 10. Bohne AV et al (2007) Faithful transcription initiation from a mitochondrial promoter in transgenic plastids. Nucleic Acid Res 35:7256–7266 11. Havey MJ et al (2002) Cucumber: a model angiosperm for mitochondrial transformation? J Appl Genet 43:1–17 12. Kumar S et al (2004) Stable transformation of the cotton plastid genome and maternal inheritance of transgenes. Plant Mol Biol 56:203–216 13. Lopez-Juez E, Pyke KA (2005) Plastids unleashed: their development and their integration in plant development. Int J Dev Biol 49:557–577 14. Lutz KA, Maliga P (2007) Construction of marker-free transplastomic plants. Curr Opin Biotechnol 18:107–114 15. Vidi PA et al (2007) Plastoglobules: a new address for targeting recombinant proteins in the chloroplast. BMC Biotechnol 7:4

Chapter 30 Appendix A: The Components of the Culture Media Víctor M. Loyola-Vargas Abstract The success in the technology and application of plant tissue culture is greatly influenced by the nature of the culture medium used. A better understanding of the nutritional requirements of cultured cells and tissues can help to choose the most appropriate culture medium for the explant used. It is also important to pay attention to a number of inaccuracies and errors which have appeared in several widely used plant tissue culture basal medium formulations. Key word: Culture media

A medium is defined as a formulation of inorganic salts and organic compounds (apart from major carbohydrate sources and plant growth regulators) used for the nutrition of plant cultures (1). The success in the technology and application of plant tissue culture is greatly influenced by the nature of the culture medium used. A better understanding of the nutritional requirements of cultured cells and tissues can help to choose the most appropriate culture medium for the explant used. Most of our knowledge of the nutrition of plant cultures comes from the solutions developed for the hydroponic culture of intact plants during the last part of the nineteenth and beginning of the twentieth centuries. The major changes made in the composition of the media since the early days have been the introduction of ammonium as nitrogen source, together with the higher amount of nitrate and potassium, as well as the use of organic additives, mainly vitamins and amino acids. Plant tissue culture provides major (macro-), minor (micro-), a carbon source, and trace amounts of certain organic compounds, notably vitamins, amino acids, and plant growth regulators (Tables 1–8). In general, the tissue culture medium must contain the 16 essential elements for plant growth (2).

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_30, © Springer Science+Business Media, LLC 2012

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Table 1 Murashige and Skoog (5) media composition Macroelements

mg/L

mM

NH4NO3

1,650

20.60

KNO3

1,900

18.80

CaCl2·2H2O

440

3.00

MgSO4·7H2O

370

1.50

KH2PO4

170

1.25

Na2EDTA

37.30

0.10

FeSO4·7H2O

27.80

0.10

Microelements H3BO3

mM

mg/L 6.20

100.0

MnSO4·4H2O

22.30

100.0

ZnSO4·7H2O

8.60

30.0

KI

0.83

5.0

Na2MoO4·2H2O

0.25

1.0

CuSO4·5H2O

0.025

0.1

CoCl2·6H2O

0.025

0.1

Organic components

mg/L

mM

myo-Inositol

100.0

555.10

Nicotinic acid

0.5

4.06

Pyridoxine·HCl

0.5

2.43

Thiamine·HCl

0.1

0.30

Glycine

2.0

26.60

Sucrose

30,000

pH

5.7–5.8

87.64 mM

Table 2 Linsmaier and Skoog (7) media composition Macroelements

mg/L

mM

NH4NO3

1,650

20.60

KNO3

1,900

18.80

CaCl2·2H2O

440

3.00

MgSO4·7H2O

370

1.50

KH2PO4

170

1.25

Na2EDTA

37.30

0.1

FeSO4·7H2O

27.80

0.1

Microelements H3BO3

mM

mg/L 6.20

100.0

MnSO4·4H2O

22.30

100.0

ZnSO4·4H2O

8.60

30.0

KI

0.83

5.0

Na2MoO4·2H2O

0.25

1.0

CuSO4·5H2O

0.025

0.1

CoCl2·6H2O

0.025

0.1

Organic components myo-Inositol Thiamine·HCl Sucrose pH

mM

mg/L 100.0

555.10

0.4

1.20

30,000

87.64 mM

5.6

Table 3 Gamborg et al. (8, 9) media composition Macroelements

mg/L

mM

134

1.0

2,528

25.0

CaCl2·2H2O

150

1.0

MgSO4·7H2O

250

1.0

NaH2PO4·H2O

150

1.1

(NH4)2SO4 KNO3

Na2EDTA

37.30

0.1

FeSO4·7H2O

27.80

0.1 (continued)

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Table 3 (continued) mg/L

mM

3.0

50.0

MnSO4·H2O

10.0

60.0

ZnSO4·7H2O

2.0

7.0

KI

0.75

4.5

Na2MoO4·2H2O

0.25

1.0

CuSO4·5H2O

0.025

0.1

CoCl2·6H2O

0.025

0.1

Microelements H3BO3

Organic components myo-Inositol

mM

mg/L 100.0

555.10

Nicotinic acid

1.0

8.12

Pyridoxine·HCl

1.0

4.86

Thiamine·HCl

10.0

Sucrose pH

20,000

30.0 58.42 mM

5.5

Table 4 Phillips and Collins (10) media composition Macroelements

mg/L

mM

NH4NO3

1,000

12.5

KNO3

2,100

20.8

CaCl2·2H2O

600

4.1

MgSO4·7H2O

435

1.8

KH2PO4

325

2.4

NaH2PO4·H2O

85

0.6

FeSO4·7H2O(EDTA)

25.0

0.1 (continued)

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Appendix A: The Components of the Culture Media

411

Table 4 (continued) mg/L

mM

5.0

82.0

MnSO4·H2O

15.0

90.0

ZnSO4·7H2O

5.0

17.5

KI

1.0

6.0

Na2MoO4·2H2O

0.4

1.7

CuSO4·5H2O

0.1

0.4

CoCl2·6H2O

0.1

0.4

Microelements H3BO3

Organic components

mM

mg/L

myo-Inositol

250.0

1,400.0

Pyridoxine·HCl

0.5

2.43

Thiamine·HCl

2

6.0

Sucrose

25,000

pH

73 mM

5.8

Table 5 White (11, 12) media composition Macroelements

mg/L

mM

80

0.79

300

1.27

65

0.87

CaCl2·2H2O

440

3.00

MgSO4·7H2O

720

2.92

NaH2PO4·H2O

19

0.13

200

1.40

KNO3 Ca(NO3)2·4H2O KCl

Na2SO4 Fe2(SO4)3

2.5

0.006 (continued)

412

V.M. Loyola-Vargas

Table 5 (continued) Microelements

mg/L

mM

H3BO3

1.5

24.2

MnSO4·4H2O

7.0

31.3

ZnSO4·7H2O

3.0

10.4

KI

0.75

4.5

MoO3

0.0001

0.007

CuSO4·5H2O

0.001

0.004

Organic components

mg/L

mM

Nicotinic acid

0.5

4.0

Pyridoxine·HCl

0.1

0.5

Thiamine·HCl

0.1

0.3

Glycine

3.0

40.0

Sucrose

20,000

pH

58.42 mM

5.5

Table 6 Nitsch and Nitsch (13) media composition Macroelements

mg/L

mM

NH4NO3

720

9.0

KNO3

950

9.4

CaCl2

166

1.5

MgSO4·7H2O

185

0.75

KH2PO4

68

0.5

Na2EDTA

37.2

0.1

FeSO4·7H2O

27.8

0.1

Microelements

mg/L

mM

H3BO3

10

161.7

MnSO4·4H2O

25

112.1

ZnSO4·7H2O

10

42.8

Na2MoO4·2H2O

0.25

1.0

CuSO4·5H2O

0.025

0.1 (continued)

30

Appendix A: The Components of the Culture Media

413

Table 6 (continued) Organic components myo-Inositol

mM

mg/L 100.0

555.10

Nicotinic acid

5.0

Pyridoxine·HCl

0.5

2.43

Thiamine·HCl

0.5

1.50

Glycine

2.0

26.60

Folic acid

0.5

1.1

Biotin

0.05

0.2

Sucrose pH

20,000

40.6

58.42 mM

5.5

Table 7 Schenk and Hildebrandt (14) media composition Macroelements

mg/L

mM

KNO3

2,500

24.72

MgSO4·7H2O

400

1.63

NH4H2PO4

300

2.60

CaCl2·2H2O

200

1.36

Na2EDTA

20

0.053

FeSO4·7H2O

15

0.054

Microelements

mg/L

mM

MnSO4·H2O

10.0

59.17

H3BO3

5.0

80.86

ZnSO4·7H2O

1.0

3.47

KI

1.0

6.02

CuSO4·5H2O

0.2

8.00

Na2MoO4·2H2O

0.1

0.41

CoCl2·6H2O

0.1

0.42 (continued)

414

V.M. Loyola-Vargas

Table 7 (continued) Organic components myo-Inositol

mM

mg/L 1,000.0

5,500.6

Nicotinic acid

5.0

40.6

Thiamine·HCl

5.0

14.8

Pyridoxine·HCl

0.5

Sucrose pH

30,000

2.43 58.42 mM

5.9

Table 8 Kao and Michayluk (6) media composition. This medium is filter sterilized Macroelements

mg/L

NH4NO3

600

KNO3

1,900

CaCl2·2H2O

600

4.08

MgSO4·7H2O

300

1.21

KH2PO4

170

1.25

Sequestrene® 330Fe

28

Microelements H3BO3

mg/L

mM 7.49 18.80

–

mM

3.00

48.5

MnSO4·H2O

10.00

59.2

ZnSO4·7H2O

2.00

7.0

KI

0.75

4.5

Na2MoO4·2H2O

0.25

1.0

CuSO4·5H2O

0.025

0.1

CoCl2·6H2O

0.025

0.1 (continued)

30

Appendix A: The Components of the Culture Media

Table 8 (continued) Vitamins

mg/L

mM

myo-Inositol

100.0

555.10

Nicotinamide

1.0

8.19

Pyridoxine·HCl

1.0

4.86

Thiamine·HCl

1.0

3.00

Calcium d-pantothenate

1.0

4.20

Folic acid

0.4

0.90

p-Aminobenzoic acid

0.02

0.15

Biotin

0.01

0.04

Choline chloride

1.00

7.16

Riboflavin

0.20

0.53

Ascorbic acid

2.00

11.35

Vitamin A

0.01

0.03

Vitamin D3

0.01

0.02

Vitamin B12

0.02

0.01

Organic acids

mg/L

mM

Sodium pyruvate

20.0

181.8

Citric acid

40.0

208.2

Other sugars and sugar alcohols

mg/L

mM

Fructose

250.0

1.38

Ribose

250.0

1.66

Xylose

250.0

1.66

Mannose

250.0

1.38

L-Amino

acids

mg/L

All are used at a concentration of 0.1 mg/L, except: Glutamine 5.6 Alanine 0.6

mM 38.3 6.7 (continued)

415

416

V.M. Loyola-Vargas

Table 8 (continued) mg/L

mM

Nucleic acid bases Adenine Guanine Thymine Uracil Hypoxanthine Xanthine

0.10 0.03 0.03 0.03 0.03 0.03

0.74 0.20 0.24 0.27 0.22 0.19

Other

mg/L

mM

Vitamin-free casamino acid

250.0

–

L-Amino

acids

Coconut watera

20.0 mL/L

–

Sucrose

20 g/L

58.40 mM

Glucose

10 g/L

55.49 mM

pH

5.6

a

From mature fruits; heated to 60°C for 30 min

The most important difference among media may be the overall salt level. There seems to be basically three different media types by this classification: high salt (e.g., Murashige and Skoog medium, Table 1), intermediate level (e.g., Nitsch and Nitsch, Table 6), and low salt media (e.g., White, Table 5). Researchers quickly found that the addition of “complexes” to the basic medium frequently resulted in successful growth of the tissues and organs. Some of these complexes have included green tomato extract, coconut milk, orange juice, casein hydrolysate, yeast, and malt extract (2). It is very important when a medium is chosen; take into account that some of the components of the culture media are not only a nutriment: some of them can have a very deep influence not only in the growth of the cultures, but also in the differentiation process. Another important fact is that vigorous colonies of callus tissue required more nutriments than slowly growing ones, while the situation can be reverse for other nutriments. It is also important to pay attention to a number of inaccuracies and errors which have appeared in several widely used plant tissue culture basal medium formulations (3, 4). The exact hydration of the iron salt and molar equivalence of iron and its chelating agent since inconsistencies exist in popular commercial preparations for several common basal media, over and above those found in the primary literature. Even the primary literature can

30

Appendix A: The Components of the Culture Media

417

have some mistakes (5) or the same name is used to designate the same medium. There have been many different versions presented in print either by White or his coworkers (4). Minor variations in medium composition can determine the success of failure of certain protocols. The excesses of chelating agent, although small, may influence micronutrient availabilities. Investigators should examine original papers carefully and compare them with commercial formulations, when seeking details on a given nutrient or medium. In relation with the Kao and Michayluk medium, the presence of vitamin-free casamino acid and the coconut water is essential for the culture of protoplasts, but they are not necessary for the culture of cells. This medium is one of the most complex between all the media used in plant tissue culture. It is used mainly for the growth of very low cell density cultures, as well as protoplasts in liquid media (6). References 1. George EF (1993) Plant propagation by tissue culture. Part 1. The technology, 2nd edn. Exegetics Limited, Great Bretaña 2. Conger BV (1980) Cloning agricultural plants via in vitro techniques. CRC, Boca Raton, FL 3. Wallace RJ (1992) Rumen microbiology, biotechnology and ruminant nutrition: the application of research findings to a complex microbial ecosystem. FEMS Microbiol Lett 100:529–534 4. Singh M, Krikorian AD (1981) White’s standard nutrient solution. Ann Bot 47:133–139 5. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497 6. Kao KN, Michayluk R (1975) Nutritional requirements for growth of Vicia hajastana cells and protoplasts at a very low population density in liquid media. Planta 126:1095–110 7. Linsmaier EM, Skoog F (1965) Organic growth factor requirements of tobacco tissue cultures. Physiol Plant 18:100–127

8. Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50: 151–158 9. Gamborg OL, Murashige T, Thorpe TA, Vasil IK (1976) Plant tissue culture media. In Vitro Cell Dev Biol Plant 12:473–478 10. Phillips GC, Collins GB (1979) In vitro tissue culture of selected legumes and plant regeneration from callus cultures of red clover. Crop Sci 19:59–64 11. White PR (1943) A handbook of plant tissue culture. Science Press Printing, Lancaster, PA 12. White PR (1963) The cultivation of animal and plant cells, 2nd edn. Ronald, New York 13. Nitsch JP, Nitsch C (1969) Haploid plants from pollen grains. Science 163:85–87 14. Schenk RU, Hildebrandt AC (1972) Medium and techniques for induction and growth of monocotyledonous and dicotyledonous plant cell cultures. Can J Bot 50:199–204

Chapter 31 Appendix B: Plant Biotechnology and Tissue Culture Resources in the Internet Víctor M. Loyola-Vargas Abstract This appendix compiles a list of useful Internet sites for cell culture scientists. A total of more than 100 sites have been selected, based on the quality of the information offered in them, as well as on their users’ friendliness. We anticipate that some of these sites will be included among the reader’s favorites (if they are not already). Key words: Internet, Plant tissue culture

1. General resources • Access excellence (http://www.accessexcellence.org/LC/ ST/st2bgplant.php) • American Ag-Tec Potato Mini-Tuber Production (http:// www.ag-tec.com/potato.htm) • Biotechnology Information Center, National Agricultural Library (http://riley.nal.usda.gov/nal_display/index.php? info_center=8&tax_level=2&tax_subject=8&topic_id= 1067&placement_default=0) • Soybean Tissue Culture and Genetic Engineering Center (http://mulch.cropsoil.uga.edu/soy-engineering/) • Cevie asbl (http://www2.ulg.ac.be/morphovg/main.htm) • Ethical, Legal and Social Aspects (ELSA) of biotechnology (http://ec.europa.eu/research/life/elsa/index.html) • Fruit Tree Research Institute, Italy (http://www.propag.org/) • Office of Biotechnology, Iowa State University (http:// www.biotech.iastate.edu/ed_resources/Laboratory_protocols. html) • Iowa State University Plant Transformation Facility (http:// www.agron.iastate.edu/ptf/) Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4_31, © Springer Science+Business Media, LLC 2012

419

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• Kitchen Culture Kits (http://www.kitchenculturekit.com/ begin.htm) • Listserv: PLANT-TC listserv/)

(http://plant-tc.cfans.umn.edu/

• National Center for Biotechnology Information (http:// www.ncbi.nlm.nih.gov/) • National Botanical Research Institute (http://www.nbrienvis. nic.in/) • National Research Council of Canada/Plant Biotechnology Institute (http://www.nrc-cnrc.gc.ca/eng/ibp/pbi.html) • NCGR-Corvallis Information—Tissue Culture (http:// www.ars-grin.gov/cor/tc.html) • Oklahoma Plant Transformation Facility (http://www.ptf. okstate.edu/) • Plant Hormones (http://www.plant-hormones.info/) • Plant Tissue Culture Research at the University of Minnesota (http://plant-tc.cfans.umn.edu/) • Plant World Explorations (http://members.ozemail.com. au/~mhempel/index.html) • Succulent Tissue Culture (http://www.succulent-tissue-culture. com/EN) • Institute for Plant Genomics and Biotechnology (http:// ipgb.tamu.edu/) • Texas A&M Plant Tissue Culture Information Exchange (http://aggie-horticulture.tamu.edu/tisscult/tcintro.html) 2. Micropropagation • Flora laboratories (http://home.alphalink.com.au/~andre/) • Growmore Bio tech (http://www.growmorebiotech.com/) • Micropropagation of Orchids (http://www.angelfire.com/ on4/angelorchids/PropagatingOrchidsnew.htm) • In Vitro Propagation (http://wwwalt.med-rz.uni-sb.de/ med_fak/physiol2/disa/invitro/000.htm) • Meyers Conservatory (http://www.troymeyers.com/) • Micropropagation unit at Royal Botanic Gardens, Kew (http://www.kew.org/science/micropropagation.html) • Oglesby Plant Laboratories (http://www.oglesbytc.com/) • Orchid Species Culture (http://www.orchidculture.com/) • The Micropropagation of Aroids (http://www.aroid.org/ horticulture/tculture.html) • Tissue culture in the homa kitchen (http://www.omnisterra. com/botany/cp/slides/tc/tc.htm)

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3. Databases • AGRICOLA (http://agricola.nal.usda.gov/help/aboutagricola.html) • Angiosperm DNA C-Values Database (http://data.kew. org/cvalues/CvalServlet?querytype=2) • Expasy (http://ca.expasy.org/) • Internet Directory for Botany (http://www.ou.edu/cas/ botany-micro/idb-alpha/botany.html) • Protein data bank (http://www.rcsb.org/pdb/home/ home.do) • Terminology Associated with Cell, Tissue and Organ Culture, Molecular Biology and Molecular Genetics (http:// www.springerlink.com/content/0g83p23206428708/) • The Arabidopsis Information Resource (http://www.arabidopsis.org/) • The WWW Virtual Library—BioScience Resources (http:// mcb.harvard.edu/BioLinks.html) • The WWW Virtual Library—Plant Science Resources (http://www.ou.edu/cas/botany-micro/www-vl/) 4. Books • Agritech Publications (http://agritechpublications.com/) –

Media and Techniques for Growth, Regeneration and Storage 2002–2005. Volume 9 of Recent Advances in Plant Tissue Culture (http://www.agritechpublications. com/rec9book.htm)

–

Micropropagation Systems and Techniques 2002–2006. Volume 10 of Recent Advances in Plant Tissue Culture ( http://www.agritechpublications.com/rec10book. htm)

–

Microbial Contaminants in Plant Tissue Culture III 2003–2007. Volume 11 of Recent Advances in Plant Tissue Culture (http://www.agritechpublications.com/ rec11book.htm)

–

Media and Techniques for Growth, Regeneration and Storage 2005–2008. Volume 12 of Recent Advances in Plant Tissue Culture (http://www.agritechpublications. com/rec12book.htm)

–

Micropropagation Systems, Techniques and Applications 2006–2010. Volume 13 of Recent Advances in Plant Tissue Culture (http://www.agritechpublications.com/ rec13book.htm)

–

Secondary Metabolite Production. Volume 14 of Recent Advances in Plant Tissue Culture (http://www.agritechpublications.com/rec14book.htm)

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–

Bibliography of Plant Micropropagation and Regeneration 2005–2009 (http://www.agritechpublications.com/bibliography.htm)

–

Plant Culture Media. Vol 1. Formulations and Uses, 1999 (http://agritechpublications.com/media1.htm)

–

Plant Culture Media. Vol 2. Commentary and Analysis, 1999 (http://agritechpublications.com/media1.htm)

5. Editorials • Annual Reviews (http://arjournals.annualreviews.org/ ;jsessionid=iBIj52VDf_R8) • Cambridge University Press (http://www.cup.cam.ac.uk/) • CRC Press (http://www.crcpress.com/) • Elsevier (http://www.elsevier.com/wps/find/homepage. cws_home) • Humana Press (http://www.humanapress.com/Index.pasp) • Kluwer (http://www.kluweronline.com/) • Springer-Verlag (http://www.springeronline.com/sgw/ cda/frontpage/0,0,0-0-0-0-EAST,0.html) • Timber Press (http://www.timberpress.com/books/index. cfm) • Vedams (http://www.vedamsbooks.com/newbot.htm) 6. Journals and newsletters • Agricell Report (http://www.agritechpublications.com/) • American Journal of Botany (http://www.amjbot.org/ current.shtml) • Biologia Plantarum issn/0006-3134/)

(http://www.kluweronline.com/

• Biotechnology Letters (http://www.kluweronline.com/ issn/0141-5492/contents) • Biotechnology Process (http://pubs3.acs.org/acs/journals/toc.page?incoden=bipret) • Canadian Journal of Botany (http://pubs.nrc-cnrc.gc.ca/ cgi-bin/rp/rp2_desc_e?cjb) • Crop Science (https://www.crops.org/publications/cs) • Current Opinion in Biotechnology (http://www. current-opinion.com/jbio/about.htm?jcode=jbio) • Current Opinion in Cell Biology (http://www.sciencedirect. com/science/journal/09550674) • Current Opinion in The Plant Biology (http://www. current-opinion.com/jpbl/about.htm?jcode=jpbl)

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• Electronic Journal of Biotechnology ( http://www. ejbiotechnology.info/) • Euphytica (http://www.kluweronline.com/issn/0014-2336/) • In Vitro Cellular and Developmental Biology—Plant (http://www.springerlink.com/content/120502/) • Journal of Experimental Botany (http://www.oxfordjournals. org/our_journals/exbotj/about.html) • Journal of Phytopathology (http://onlinelibrary.wiley.com/ journal/10.1111/(ISSN)1439-0434/issues) • Journal Plant Physiology (http://www.elsevier-deutschland. de/jpp) • Nature Biotechnology (http://www.nature.com/biotech/) • New Phytologist (http://onlinelibrary.wiley.com/journal /10.1111/(ISSN)1469-8137/issues) • Physiologia Plantarum (http://onlinelibrary.wiley.com/ journal/10.1111/(ISSN)1399-3054/issues) • Plant Biotechnology Journal (http://onlinelibrary.wiley. com/journal/10.1111/(ISSN)1467-7652/issues) • Plant Breeding (http://onlinelibrary.wiley.com/journal/ 10.1111/(ISSN)1439-0523/issues) • Plant Cell (http://www.plantcell.org/) • Plant Cell and Environment (http://onlinelibrary.wiley. com/journal/10.1111/(ISSN)1365-3040/issues) • Plant Cell Physiology (http://pcp.oupjournals.org/) • Plant Cell Reports content/100383/)

(http://www.springerlink.com/

• Plant Cell, Tissue and Organ Culture (http://www.springerlink.com/content/100327/) • Plant Growth Regulation (http://www.springerlink.com/ content/100329/) • Plant Journal (http://www.wiley.com/bw/journal. asp?ref=0960-7412) • Plant Molecular Biology (http://springerlink.metapress. com/content/100330/) • Plant Physiology (http://www.plantphysiol.org/) • Planta (http://www.springerlink.com/content/100484/) • Theoretical and Applied Genetics (http://www.springerlink. com/content/100386/) • Trends in Biochemical Sciences (http://www.sciencedirect. com/science?_ob=PublicationURL&_cdi=5180&_auth=

424

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y&_acct=C000059356&_version=1&_urlVersion=0&_ userid=2974920&_pubType=J&md5=1b4a07b34d6fe15d dacb8cd1fb738380) • Trends in Biotechnology (http://www.sciencedirect.com/ science?_ob=PublicationURL&_cdi=5181&_auth=y&_ acct=C000059356&_version=1&_urlVersion=0&_userid= 2974920&_pubType=J&md5=9efeee93233c50cb1b127c 9b14cada8d) • Trends in Cell Biology (http://www.cell.com/trends/ cell-biology/) • Trends in Genetics (http://www.sciencedirect.com/ science?_ob=PublicationURL&_cdi=5183&_auth=y&_ acct=C000059356&_version=1&_urlVersion=0&_ userid=2974920&_pubType=J&md5=d57158b47005b4a 548870531924e4cf2) • Trends in Plant Science (http://www.sciencedirect.com/ science?_ob=PublicationURL&_cdi=5185&_auth=y&_ acct=C000059356&_version=1&_urlVersion=0&_ userid=2974920&_pubType=J&md5=79e9758da731688 9a1c1ac01ec45414f) 7. PTC inside the classroom • Access Excellence (http://www.accessexcellence.org/) • Cloning Plants By Tissue Culture (http://csm.jmu.edu/ biology/renfromh/pop/pctc/cloning.htm) • Plant Cell Protoplasts (http://agronomy.unl.edu/815/ cropt.htm) • TNAU Agritech Portal (http://agritech.tnau.ac.in/ bio-tech/biotech_tc_jainirrigation.html) 8. Societies • American Phytopathological Society (http://www.apsnet. org/Pages/default.aspx) • American Society for Horticultural Science (http://www. ashs.org/) • American Society of Plant Physiologists (http://my.aspb. org/members/) • Botanical Society of America (http://www.botany.org/) • International Association for Plant Tissue Culture and Biotechnology (IAPTC&B) (http://www.danforthcenter. org/iapb-stl/) • International Association of Sexual Plant Reproduction Research (IASPRR) (http://www.iasprr.org/) • International Plant Propagators’ Society (http://www.ipps. org/)

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• Society for In Vitro Biology (http://www.sivb.org/) • The American Orchid Society (http://www.aos.org//AM/ Template.cfm?Section=Home) 9. Design and layout of a micropropagation facility • Design and Layout of a Micropropagation Facility (http:// aggie-horticulture.tamu.edu/tisscult/microprop/facilities/ microlab.html)

INDEX A Abscisic acid (ABA) ...................17, 130, 138, 183–189, 198 Acclimatization................................138, 139, 149, 158, 251, 252, 254, 255, 258 Acer pseudoplatanus .............................................................10 Adventitious buds ...........................4, 17, 250, 251, 256, 293 AFLP. See Amplified fragment length polymorphism (AFLP) Agave fourcroydes ................................3, 315, 316, 322, 350 Agrobacterium-mediated transformation ............................... 19, 357–382, 403 Agrobacterium rhizogenes ........................................ 32, 35, 36 Agrobacterium tumefaciens...................................... 5, 13, 251, 255, 359, 363, 366, 373, 379, 387, 394 amiRNAs. See artificial miRNAs (amiRNAs) Amplified fragment length polymorphism (AFLP) ..................... ..289, 293, 330, 343, 344, 347, 348, 350–353, 355 Analysis of variance (ANOVA) ...............................112–123 Androgenesis ....................................................... 13, 15, 230 ANOVA. See Analysis of variance (ANOVA) Anther .................................................................4, 5, 13, 51, 54, 166, 167, 171, 227–230, 237, 381, 386 Antibody based detection (DNA methylation) ............................. 328–329, 333 Appendix ..................................................407–417, 419–425 Aquatic plants.......................................................... 266, 268 Arabidopsis thaliana root-mediated shoot regeneration ................................................. 183, 185 Argemone mexicana ................................................ 271–276 Artificial miRNAs (amiRNAs) ............................... 304–310 Artificial target mimics .................................... 304, 307–310 Arundo donax ...........................................................153–159 Asparagus officinalis ............................................................90 Auxins ............................................................................. 287 Axillary buds..............4, 17, 97, 132, 134, 155, 156, 158, 253

B BA. See Benzyladenine (BA) Banana .................................................................4, 143–150 Benzophenanthridine-type alkaloid ........................271, 275 Benzyladenine (BA) ............................................. 32–35, 37,

110, 111, 117, 118, 121–126, 130, 144, 146, 213, 237, 238, 243, 250, 272, 273, 387, 388 Binomial data ..................................................................112 Biofuel ......................................................2, 7, 153, 154, 303 Biolistics .......................................16, 19, 359–363, 403–404 BioMINT® ......................................................................140 Bioremediation ............................................................2, 261 Bisulfite sequencing ................................................. 331, 332 Brassica campestris ............................................................... 16

C Callus............................................................ 3, 4, 11–14, 17, 29–38, 41–44, 46, 97, 101, 133, 137, 174, 175, 177–180, 184, 185, 187, 214, 219, 228, 240, 243, 248, 250, 251, 254, 260, 273, 287, 292, 293, 326, 361, 365, 371–373, 380, 404, 416 Capsicum ..................................................... 51, 227–230, 275 Castanea dentata ............................................................... 386 Castanea sativa ..................................285, 288, 291, 329, 386 Catharanthus roseus ............................ 3, 32, 34, 36–38, 82, 90 Cedar .......................................................................129–141 Cedrela odorata .......................................................... 129–141 Cell counting ................................................... 42–44, 46, 55 Cell cultures......................4, 6, 14, 15, 17–20, 29, 46, 47, 81, 82, 101, 146, 174, 248, 271, 272, 274, 275, 287, 419 Cell density............................. 30, 43, 45, 47, 49, 55, 89, 417 Cell viability ..........................................................46, 49–55 ChIP. See Chromatin immunoprecipitation (ChIP) Chloroplast transformation .....................................402–405 Chromatin .......................................278–285, 287, 290, 291, 313–315, 326, 327, 332–337 Chromatin immunoprecipitation (ChIP) ........ 314, 333–337 Chromium ........................................35, 44, 46, 55, 266, 269 Chromosome doubling ..... 161, 163, 165–166, 171, 234, 242 Clonal propagation ............. 4, 12, 13, 17, 129–141, 143, 249 Coconut water (CW) ...................11, 12, 131, 137, 416, 417 Coffea arabica .........................................3, 32, 33, 35, 37–38 Coffea canephora......................................... 3, 315, 316, 322 Colchicine ........................................... 5, 163, 165–168, 170 Continuous data ......................................................112–114 Cork oak ..................................................................385–397 Cosmos .................................................... 234–238, 240, 243 Cryoconservation.............................................................211

Víctor M. Loyola-Vargas and Neftalí Ochoa-Alejo (eds.), Plant Cell Culture Protocols, Methods in Molecular Biology, vol. 877, DOI 10.1007/978-1-61779-818-4, © Springer Science+Business Media, LLC 2012

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PLANT CELL CULTURE PROTOCOLS 428 Index Cryopreservation ............................... 6, 17, 81–91, 191–222 Cryoprotectant ........................................... 17, 90, 192, 196, 199–200, 210, 212, 218 Cryoprotection ....................................................... 191, 196, 199, 200, 202, 204, 206, 210, 212, 218 Cryostorage ....................................................... 83, 214, 215 Culture cell density ....................................................45, 317 Culture contamination .......................................... 58, 71, 72 Culture media ................................ 65, 71, 96, 131, 144, 146, 155, 185–186, 195, 217, 230, 238, 248, 250, 251, 259, 292, 360–366, 378, 387–388, 407–417, 422 CW. See Coconut water (CW)

D Data analysis............................................................110–112 Datura innoxia.............................................................. 13, 16 Dehydration ........................................81–91, 197, 198, 202, 206–208, 219, 220 Desiccation .................................... 44, 83, 91, 107, 132, 167, 175, 202, 206, 208, 220, 221, 376, 380, 381, 392 Dicamba ..................................................................130, 131 Digital camera ......................................... 100–102, 105, 106 DNA fingerprinting ........................................................344 DNA methylation ................7, 197, 277–295, 313, 326–332 Dormancy epigenetics .....................................................291 Double-haploids .........................1, 5, 15, 161–172, 227, 228 Doubling time (dt) .................................... 36, 37, 45, 47–48 dt. See Doubling time (dt) Duplication time ...............................................................38

E Elicitation ........................................................ 6, 31, 50, 274 ELISA. See Enzyme linked immunosorbent assay (ELISA) Embryo dissection ...........................................................177 Embryogenesis ..............................................3, 4, 15, 17, 19, 95, 132, 133, 137–139, 173–180, 283, 285–289, 292, 293, 325, 360, 378, 386, 390–391, 393 Embryo germination ....................................... 368, 388, 393 Embryo maturation ......................85, 88, 178–180, 184, 388 Embryo rescue ................................................... 15, 235, 238 Embryos ..................................................2, 10, 30, 51, 81, 96, 112, 132, 162, 174, 184, 194, 228, 235, 283, 309, 322, 329, 360, 386 Encapsulation ...............................81–91, 197, 200, 206–210 Endophytes................... 58–60, 62, 64, 65, 67, 70, 71, 76, 77 Enzyme linked immunosorbent assay (ELISA) ..................... 17, 61–63, 67, 69, 70, 76, 328 Epigenetics ...............................6–7, 277–295, 314, 326, 337 Epigenetic variation............................................. 7, 326, 343 Exocarpus cupressifornus ...................................................... 13

F Fagaceae ..................................................................385, 386 Flowering epigenetics .............................. 282–285, 287, 295 Freezing ................................................................ 82–86, 88, 89, 194, 196, 200, 210–212, 219, 361 Fusarium oxysporum .................................................. 272–275

G Gene silencing .................................280, 289, 290, 304–306, 308, 309, 402 Genetic transformation .................................. 5–7, 248, 249, 251–253, 255–259, 385–397 Genetic variation ......................................... 1, 293, 298, 326 Gene transfer .....................................................................19 Genome wide DNA methylation ....................................330 Genomic profile of histone posttranslational modifications (PTMs) ........................ 279, 281, 282, 313, 315, 333–337 Genomic profile of nucleosome distribution ...................336 Germplasm ............................ 2, 6, 17, 19, 83, 130, 161–165, 167–171, 175, 191, 193, 194, 200, 208, 211, 215, 249 Germplasm storage................................................13, 16–18 Giant reed (Arundo donax) .....................................153–159 Giberellic acid (GA3)............................... 130, 131, 137, 141 Global DNA methylation........................278, 288, 289, 291, 326–329, 333 Grafting ..................................61, 62, 65, 132–134, 136, 140 Growth curves .............................................................30–32 Growth cycle ................................................... 31, 36, 38, 43 Growth index .........................................7, 37, 38, 42, 45–47

H Haberlandt .................................................... 2, 9, 10, 12, 20 Hairy roots .................................................. 29–39, 248, 265 Haploid embryos ............................................. 165, 228, 386 Haploids .................................................... 15, 161–172, 227 Haploidy .................................................. 162–164, 167, 227 Heavy metals ......................18, 247–249, 258–262, 265–270 Herbicide resistance................................. 367, 376, 377, 394 Histochemical staining ............................................101–104 Histology ...................................................................96, 102 Histone H3 methylation ......................... 313–315, 318, 322 Histone isolation ............................................. 316–317, 319 Histone methylation .................................... 7, 284, 313–323 Histones ..........................................278, 279, 281–282, 294, 313–315, 319, 322, 323, 326, 327, 332, 333, 336 Homozygous ..........................................5, 51, 161, 171, 227 Hybrid plants............................ 1, 13, 16, 228, 235, 241, 243

PLANT CELL CULTURE PROTOCOLS 429 Index I Immature embryos ........... 174, 175, 177, 178, 180, 360, 368 Immature seed rescue ...................................... 236, 238–240 Internet plant tissue culture resources......................419–425 Inter-specific hybrids ......................................... 13, 233–244 Isogenic ...............................................................................5

144, 146, 149, 155, 156, 159, 176, 185–187, 229, 230, 236–238, 243, 250, 251, 253, 259, 261, 266–268, 327–328, 330, 331, 333, 360, 361, 364, 365, 387, 408, 416 Musa spp ................................................................... 143, 211

N

Jatropha curcas ............................................... 3, 31, 32, 35–37

Nicotiana glauca ............................................................ 10, 13 Nicotiana langsdorffii .................................................... 10, 13 Nothofagus alpina .............................................................. 386

K

O

Kalanchoe ........................................................ 235, 237–239

Organ culture .........................................1, 3–4, 58, 421, 423 Organelle transformation ........................................401–405 Organogenesis ............................... 13, 14, 30, 110, 117, 183, 184, 219, 292, 326, 329, 332 Ornamental plants ...................................................233–244 Ovary.............................12, 15, 234, 235, 237, 239, 240, 244 Ovule ...................................... 12, 13, 15, 237, 238, 240, 243

J

L Lead ............................................................19, 90, 118, 119, 121, 166, 169, 170, 219, 220, 266, 269, 285, 286, 289, 307, 315, 326, 331, 336, 361, 364 Linum austriacum ............................................................... 10 Linum perenne .................................................................... 10 Logistic regression ............................112, 114, 119, 120, 123

M Macleaya cordata ................................................................. 11 Manganese ..............................................................266, 269 Mean separation test .......................................................114 Medicago sativa ................................................................... 82 Meristems.................................4, 11, 97, 174, 184, 191–222 Metal removal..........................................................267–269 Methyltransferases ............ 279, 282, 285, 291, 295, 314, 315 Mexican Tuxpeño ............................................................175 Microarray-based DNA methylation profiling ................329 Microprojectile bombardment ...........................................16 Micropropagation ................................................. 1, 3, 4, 17, 18, 58, 66, 67, 72–74, 76, 77, 81, 97, 130, 132, 135–137, 139, 140, 143–150, 196, 293, 316, 420–422, 425 MicroRNA( miRNA), 7, 303–310, 337 Microspore ................................. 5, 51, 52, 54, 184, 228, 230 miRNA. See MicroRNA( miRNA) Mitochondria transformation ..........................................402 Molecular markers ............................320, 329, 332, 343–355 Morphogenesis ................... 2, 14, 15, 19, 287, 292, 304, 326 MS medium. See Murashige and Skooog medium (MS medium) Multiple comparison tests .......................................114, 115 Multiple range tests ..........................114–115, 120, 121, 123 Murashige and Skooog medium (MS medium), 12, 31–37, 51, 111, 112, 114, 116, 119, 121, 124, 125, 131, 135, 137, 138,

P Packed cell volume (PCV) ..........................................42, 45 Papaveraceae ............................................................271–276 Papaver somniferum ...................................................... 13, 90 PCR-RFLP of ITS ......................................... 236, 240–241 PCV. See Packed cell volume (PCV) Petunia x hybrida ...................................... 110, 121, 124, 125 Photography ..............................................................95–107 Photomicrography ........................................... 100, 101, 105 Phytagel ................................................... 145, 364, 365, 378 Pinus ......................................................................4, 130, 328 Plant cell reprogramming epigenetics......................291–294 Plant preservative media (PPM®) ............................131, 133 Plant regeneration .......................................... 85, 86, 88, 89, 173–180, 184, 228, 230, 256 Plastid transformation .....................................................405 Poisson regression ............................................ 112–114, 120 Populus ............................................... 130, 249–253, 255–261 Primula ..................................................... 234–238, 241, 243 Protoplasts ................................ 3, 4, 13, 14, 16, 30, 417, 424 PTMs. See Genomic profile of histone posttranslational modifications (PTMs)

Q Quercus robur .................................................................... 386 Quercus suber ............................................................. 385–397

R Radioimmunoassay ............................................................17 Raphanus sativus................................................................. 16

PLANT CELL CULTURE PROTOCOLS 430 Index Regional DNA methylation levels ...................................332 Regression analysis ...........................112, 117, 120, 124, 125 Rejuvenation............................................................130, 287 Restriction enzyme DNA methylation pattern .......329–330 RNAi ....................................................................... 289, 308 Robinia pseudoacacia ........................................................... 10 Root cultures ..........................2, 10, 30, 35–36, 38, 265–269 Roots ............................................... 2, 10, 29–38, 60, 88, 95, 116, 134, 149, 158, 169, 179, 183–189, 219, 235, 248, 265, 274, 288, 304, 315, 362, 395

S Saccharum officinarum ....................................................... 153 Salix capraea ....................................................................... 10 Sanguinarine............................................................271–276 Scirpus americanus ..................................................... 266–269 SCV. See Settled cell volume (SCV) Secondary metabolites ............................... 2, 17–19, 30, 421 Self-pollination....................................................... 161, 164, 166–168, 171, 234, 237, 242, 243 Sequencing DNA methylation ................................331–332 Settled cell volume (SCV) ...........................................42, 45 Sexual embryogenesis epigenetics............................285–287 Shoots................................................................4, 10, 11, 97, 110, 112, 113, 117, 119–126, 131, 132, 134–140, 144, 145, 147–149, 158, 159, 164, 167, 171, 179, 184, 187, 188, 194, 196, 197, 205–207, 212, 214–216, 220, 221, 235, 249–251, 253–256, 284, 291, 293, 371, 372, 374, 375, 380, 390, 391 siRNA (small interfering RNA) ..................... 280–281, 295, 305–337 Small RNAs (miRNA and siRNA) ........................ 281, 305, 306, 309, 337 Solanum lycopersicum ........................................................... 51 Somaclonal variants .................................................249, 293 Somaclonal variation ............................................ 15, 18, 82, 249, 250, 253–255, 293–295, 327, 329, 337, 343 Somatic cell fusion...............................................................2 Somatic embryogenesis ...................3, 4, 15, 17, 19, 132, 133, 137–139, 173–180, 283, 287, 292, 293, 325, 386, 391 Somatic embryogenesis epigenetics .................................283 Somatic embryos .......................................... 11, 30, 97, 112, 138, 174, 179, 287, 371, 387, 391 Somatic hybrids ...................................................................5 Specific growth rate ............................................... 45, 47, 48

Statistical analysis ............................................ 110–112, 293 Statistics .......................................................... 109–126, 262 Sugarcane ........................................................ 153, 154, 402 Suspension cultures .................................... 3, 29–38, 41–43, 45, 46, 50–53, 101, 102, 271–276, 293, 334, 337

T Tagetes erecta ....................................................................... 11 Temporary immersion .............................................131, 139 Thidiazuron (TDZ) ........................110, 111, 119, 121–124, 144, 243, 250 Tissue culture-induced phenotypic variations .........294–295 Totipotency................................. 4, 10, 12, 13, 285, 286, 315 Tradescantia reflexa ............................................................. 13 Transcription factor PTMs (posttranslational modifications) ..............................................336–337 Transformed plants ..........................................................387 Transgenic plants ........................... 5, 19, 175, 248, 249, 308, 309, 359, 366, 367, 371–377, 380, 381, 386, 397 Tree development ....................................................277–295 Tree genetic transformation.............................................394 Trees ........................................ 10, 17, 18, 65, 130–133, 139, 140, 154, 240, 247–262, 283, 288, 290, 291, 386–388 Triticum aestivum (wheat).................249, 252, 260, 359, 372 Typha latifolia ........................................................... 265, 268

U Ulmus campestre .................................................................. 10

V Vaccinium pahalae.......................................................... 82, 90 Virus elimination ................................................... 12, 62, 68 Vitis...... ............................................................. 83, 85, 89, 90 Vitrification .................. 81–91, 191, 200–206, 208–213, 220

W Wheat transformation .....................................................359

Y Yeast extract .................... 12, 35, 36, 251, 273, 275, 363, 388

Z Zea mays ........................................................... 153, 161, 177